(updated: Thu Sep 13 12:30:58 2018)

In these diagrams sets of entries from the database are clustered to show their interface (left) and overall structural (right) similarity. Mouse over complex names to check their SCOP superfamilies and click on the L links to see their structure-based sequence logos. Please check the help page for more details.


> 1a0a_B:PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

  
  RG--HGKT----EA----RCRC------   L                 +----1a0a_B    
                                             +-----4 
  ----HG------ET----RTRG------   L     +-----5     +----5v0l_A    
                                       !     ! 
  ----HG----ITEC----RCRG------   L   +-6     +----------5nj8_D    
                                     ! ! 
  --QG------VTEC----RCRG----QG   L   ! !           +----1an4_A    
                                     ! +-----------3 
  --------HGST--ITET----RCRG--   L --7             +----4h10_A    
                                     ! 
  ----HGNT----EC----RCRG------   L   !                  +1nkp_E    
                                     !                +-1 
  ----HGNT--LGEC----RCRC------   L   +----------------2 +5i50_B    
                                                      ! 
  ----HGNT--MTEA----RCRG------   L                    +-1nlw_D    
                                   


> 1a6y_A:REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

  
  --HAEC--KG--RGRG----FT   L              +1a6y_A    
                               +----------6 
  ----EC--KA--RGRG------   L   !          +4nqa_I    
                               !  
  ----EC--KG--KGRA------   L   !           +5l0m_A    
                               !     +-----1 
  ----EC--KG--KGRG------   L   !     !     +2ff0_A    
                             -16     !  
  ----EA--KG--RTRG------   L   !     !          +1kb2_B    
                               !     !        +-3 
  ----EC--KG--RGRG------   L   !     !        ! +2nll_B    
                               !     !        !  
  ----DG--KG--RTRG------   L   !     !     +-12      +3cbb_A    
                               !     !     !  !    +-2 
  CA--EC--KG--KGRG------   L   +----15     !  !  +-8 +1cit_A    
                                     !     !  !  ! ! 
  --HGECAGKGAAKGRT------   L         !     !  +-11 +1lo1_A    
                                     !  +-13     !  
  --HC----KGVT--RG--RT--             !  !  !     ! +3g9m_B    
                                     !  !  !     +-9 
  ----EA--KG--RTRTRT----             !  !  !       +2han_B    
                                     !  !  !  
  ----EC--KG--KGRG------   L         !  !  +--1dsz_B    
                                     +-14  
  --------KGVT--RG--RC--   L            !      +2c7a_B    
                                        !    +-4 
  --------KGVT--RG------   L            !  +-7 +5cbz_E    
                                        !  ! ! 
  --------KAVA--RA------   L            +-10 +5e69_A    
                                           !  
  ----ET--KGAT--RG------   L               ! +1lat_A    
                                           +-5 
  --------KGVT--RG------                     +5emc_A    
                             


> 1ais_B:TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

  
  ------VCRG----------                                  +-1c9b_M    
                                         +--------------2 
  QT----EG------------       +-----------4              +-6f40_V    
                             !           ! 
  --ACRC--------------   L   !           +----------------4roc_A    
                           --5 
  ----------NT--NAIARG   L   !                            +4cyc_B    
                             !             +--------------1 
  ----------NCITNARGRG   L   +-------------3              +6fqq_E    
                                           ! 
  ----------NCICNARGRG   L                 +--------------6fqp_B    
                           


> 1am9_A:HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER

  
  ------HGNT--IAEC----YCRG------   L                 +1am9_A    
                                                   +-1 
  ------------HGNT--LGEC----RCRC   L            +--3 +5i50_B    
                                                !  ! 
  KT----HGNT----EC----RCRG------   L          +-6  +-1nkp_A    
                                              ! ! 
  --HGNT--MTEA----RCRG----------   L          ! !   +1nlw_D    
                                       +------7 +---2 
  NT----------------------------   L   !      !     +1nkp_E    
                                       !      ! 
  --RT------NT--RGEC----RCQT----       !      !   +--2ypa_A    
                                     --8      +---5 
  ----NT----EC----RCRT----------   L   !          +--4ati_B    
                                       ! 
  ------HGST--ITET----RCRG------   L   !           +-4h10_A    
                                       +-----------4 
  ------HG------ET----RTRG------   L               +-5v0l_A    
                                     


> 1an4_A:STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF

  
  --QG----VTECRCRGQG   L             +-----1an4_A    
                                     ! 
  ----HGSTITETRCRG--   L          +--4     +4h10_A    
                                  !  ! +---1 
  RT----NTRGECRCQT--              !  +-3   +2ypa_A    
                           +------5    ! 
  ----HG--ITECRCRG--   L   !      !    +---5nj8_D    
                           !      ! 
  ----HGNTIAECRCRT--   L --6      !     +--4ati_B    
                           !      +-----2 
  ----HGNTMTEARCRG--   L   !            +--1nlw_D    
                           ! 
  RG--HGKT--EARCRC--   L   +---------------1a0a_B    
                         


> 1au7_A:PIT-1 MUTANT/DNA COMPLEX



> 1awc_A:MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA

  
  --------KT--RGAT--RGYT------------   L                  +------1awc_A    
                                                          ! 
  ------DCKT--RG----RGYA------------   L             +----5      +1dux_F    
                                                     !    !    +-1 
  --------KT--RGAT--RGYA------------   L             !    +----3 +1bc8_C    
                                               +-----6         ! 
  --------KT--RGSA--RGQA------RA----   L       !     !         +-1yo5_C    
                                               !     ! 
  --------ST--------RTQT--MT--------   L   +---7     !          +5d8k_B    
                                           !   !     +----------2 
  --KTHG----------------------------       !   !                +5hdn_C    
                                         --8   ! 
  TT----KATTQTTG----LTRT----KA--FTYT   L   !   +-----------------2p7c_B    
                                           ! 
  ------------NT--RGCT--NGST--------   L   !                   +-1if1_B    
                                           +-------------------4 
  ------------------------RG--------                           +-4hly_B    
                                         


> 1b3t_A:EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX

  
  WGFTRTNTKGFT------KTTGYCNG--RT----------------------------------------   L                          +1b3t_A    
                                                                                    +-----------------1 
  WCFT----KG--------KGTAYCNG--RT----------------------------------------   L   +----2                 +5t7x_B    
                                                                               !    ! 
  ------------TAFCSG--------------LATGSG--VGFA------------RAECACKCSCTAKC   L --3    +-----------------5tkz_B    
                                                                               ! 
  --------------------------VC--RC------RC----PANAFAKCKCDC--------------   L   +----------------------3vke_A    
                                                                             


> 1b72_A:PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX



> 1bc8_C:STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

  
  ----------KT--RGAT--RGYA--------------   L                           +--1bc8_C    
                                                                       ! 
  --------DCKT--RG----RGYA--------------   L                  +--------6   +1dux_F    
                                                              !        ! +-1 
  ----------KT--RGAT--RGYT--------------   L                  !        +-4 +1awc_A    
                                                       +------8          ! 
  ----------KT--RGSA--RGQA------RA------   L           !      !          +-1yo5_C    
                                                       !      ! 
  ----------ST--------RTQT--MT----------   L           !      !          +5d8k_B    
                                                    +--9      +----------3 
  ----KTHG------------------------------            !  !                 +5hdn_C    
                                                    !  ! 
  ------------NA----RAHT--STLT----------   L        !  !            +-----2a07_K    
                                               +---10  +------------7 
  --TT----KATTQTTG----LTRT----KA--FT--YT   L   !    !               +-----2p7c_B    
                                               !    !  
  ----------------NT--CT--NGST----------   L   !    !                    +1if1_B    
                                             -11    !                  +-2 
  --------KG----ATNT--CT----SC----------   L   !    +------------------5 +2irf_L    
                                               !                       ! 
  --------------------------RG----------       !                       +--4hly_B    
                                               !  
  RT--------------------------------YG--   L   +--------------------------5vfx_A    
                                             


> 1bf5_A:TYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX

  
  --------KCEC--STNTVGSTQT   L                              +1bf5_A    
                                                   +--------1 
  --------------STNT----QT       +-----------------2        +1bg1_A    
                                 !                 ! 
  ------------KAVTHG--NTQT   L --3                 +--------4y5w_B    
                                 ! 
  NCTTATRG----------------   L   +---------------------------2dgc_A    
                               


> 1bg1_A:TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX

  
  ------------STNT----QT                                 +-1bg1_A    
                                                 +-------1 
  --------KC--STNTVGSTQT   L   +-----------------2       +-1bf5_A    
                               !                 ! 
  ----------KAVTHG--NTQT   L --3                 +--------4y5w_B    
                               ! 
  NCTTATRG--------------   L   +---------------------------2dgc_A    
                             


> 1c9b_M:CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP)

  
  ----------VCRG----------                                 +--1c9b_M    
                                             +-------------1 
  QT--------EG------------         +---------2             +--6f40_V    
                                   !         ! 
  --ACRC------------------   L   +-3         +----------------4roc_A    
                                 ! ! 
  --------------NCITNARGRG   L --4 +--------------------------6fqq_E    
                                 ! 
  ------RGYG--------------       +---------------------------1qbj_C    
                               


> 1cf7_A:STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

  
  RC----------------------------------RGRG--YC----------------------------   L                                       +1cf7_A    
                                                                                                      +--------------1 
  ----------TTQT----------------------------------------------------------   L                        !              +3gpl_A    
                                                                                                   +-16  
  --------------------------------ST--PTTC----QG------RG------------------   L                     !  !  +-------------1f5t_A    
                                                                                                   !  +-14  
  ----------------------ST--------STQAQGST--SART------------------KT------   L                     !     +-------------5trd_B    
                                                                                                   !  
  --------------------------------------------------YGRG------------------                         !                   +4wcg_B    
                                                                                                   !                 +-3 
  --------------LAHAKARA------------------------------------------------IA                         !              +--5 +6dta_A    
                                                                                                   !              !  ! 
  ------------------------SGQG------YCNC----------------------------------                         !              !  +2ve9_C    
                                                                                                +-19            +-7 
  --------------------------------------------------YG--------------------                      !  !            ! !  +2heo_D    
                                                                                                !  !            ! +--4 
  --------------------------------------------------YG--------------------                      !  !        +---9    ! +4ka4_B    
                                                                                                !  !        !   !    +-2 
  ------------------------------------KGTA----TA------RG------------------   L                  !  !        !   !      +1xsd_A    
                                                                                                !  !  +----12   ! 
  ------------------------RG------STRGMCTT--RT----------------------------   L                  !  !  !     !   +-----4u0y_B    
                                                                                             +-21  !  !     !  
  ----------------------------------RGSTRT--STHG------------------RA------   L               !  !  !  !     !  +------3zpl_B    
                                                                                             !  !  +-18     +-10  
  --------------------------------TT--PTTC--STNT------------------RT------   L               !  !     !        +------4lln_I    
                                                                                             !  !     !  
  --------------------------------STKTPTTT--FT------------------RA--------   L               !  !     !    +----------4aso_F    
                                                                                             !  !     +---13  
  --------------------------------STQTPT--TTRG--------------------HT------   L               !  !          +----------5xxp_A    
                                                                                          +-22  !  
  --SGITMTPT------------------RT------------------------------------------   L            !  !  +-------------------5fmf_V    
                                                                                          !  !  
  ------------------------------------------NAST--RTHT--ST----------------   L            !  !      +---------------3l2c_A    
                                                                                          !  !      !  
  ------------------------------------------NA----RAHT--STLT--------------   L            !  !  +--17         +-----2a07_K    
                                                                                          !  !  !   !       +-8 
  ----------------------TT------------KATT--QTTG----LTRT----KA------FTYT--   L         +-24  !  !   +------11 +-----2p7c_B    
                                                                                       !  !  +-20           !  
  ------------------------------------DCKT----RG----RGYA------------------   L         !  !     !           +-------1dux_F    
                                                                                       !  !     !  
  ------------------------------NG----RGRG--YC----------------------------   L         !  !     +-------------------1cf7_B    
                                                                                       !  !  
  ------------------------------------HT----RTITYT------------------------   L      +-25  !          +-------------4kfc_B    
                                                                                    !  !  !  +------15  
  ----------------------------------RG----DTVT----STRG--------RC----------   L      !  !  +-23       +-------------4nhj_A    
                                                                                    !  !     !  
  ------------------------------------NTVC--ECSTYT--STYC------RA----------   L      !  !     +---------------------5ed4_A    
                                                                                 +-26  !  
  --------------------------------TTLTECTA--STRG--------------------------   L   !  !  !                    +---4i2o_B    
                                                                                 !  !  +--------------------6 
  --------------------------------ITRGECSC--SGKG--------------------------   L -27  !                       +---5i2d_R    
                                                                                 !  !  
  --------KC------------------------MGSGTT--TTYC--------------------------   L   !  +--------------------------5f7q_C    
                                                                                 !  
  --------------------------------------------IT----QTNA----RG------------   L   +---------------------------6dfy_D    
                                                                               


> 1cf7_B:STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

  
  ------------NGRGRGYC--------------------   L                       +-------1cf7_B    
                                                         +-----------4 
  --------------QA------------------------   L           !           +-------2vla_A    
                                                         ! 
  ------------------NA--RAHT--STLT--------   L           !             +-----2a07_K    
                                                 +-------7           +-3 
  ----TT--------KATTQTTG--LTRT----KA--FTYT   L   !       !   +-------5 +-----2p7c_B    
                                                 !       !   !       ! 
  KAFA------------------------------MC----       !       !   !       +-------3aaf_B    
                                                 !       +---6 
  --------------RGRGYC--------------------   L --8           !           +---1cf7_A    
                                                 !           +-----------2 
  ------------------------YGRG------------       !                       ! +-4wcg_B    
                                                 !                       +-1 
  ------------------------YG--------------       !                         +-2heo_D    
                                                 ! 
  ------QGVCRC----------------------------   L   +---------------------------5dwa_A    
                                               


> 1cit_A:DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B

  
  CA--EC--KG--KGRG------RT--RT--   L                         +-1cit_A    
                                                          +-12  
  ----EA--KG--RTRG--------------   L                      !  ! +1kb2_B    
                                                          !  +-1 
  ----EC--KG--RGRG------KA------   L                   +-14    +2nll_B    
                                                       !  !  
  ----EA--KG--RTRTRT------------                       !  !  +--2han_B    
                                                       !  +-13  
  ----DG--KG--RTRG--------------   L                   !     !  +3cbb_A    
                                                    +-15     +--3 
  ----EC--KG--KGRG--------------   L                !  !        +1dsz_B    
                                                    !  !  
  --HGECAGKGAAKGRT--------RT--RC   L                !  !   +1lo1_A    
                                                    !  +---9 
  ----EC--KG--KGRA----RT--------   L                !      ! +5l0m_A    
                                                    !      +-2 
  ----EC--KG--KGRG----RC--------   L                !        +2ff0_A    
                                       +-----------16  
  --------KGVG--RG--RA----------   L   !            !         +3g6t_A    
                                       !            !       +-5 
  --HAEC--KG--RGRG--------------   L   !            !       ! +1a6y_A    
                                       !            !       !  
  --------KGVT--RG--------------   L   !            !    +-10   +5cbz_E    
                                       !            !    !  ! +-7 
  --------KAVA--RA--------------   L   !            !    !  ! ! ! +5e69_A    
                                     -17            !    !  +-8 +-4 
  --------KGVT--RG--------------   L   !            +---11    !   +2c7a_B    
                                       !                 !    ! 
  --HC----KGVT--RG--------------       !                 !    +3g9m_B    
                                       !                 !  
  ----ET--KGAT--RG--------------   L   !                 ! +1lat_A    
                                       !                 +-6 
  --------KGVT--RG--------------       !                   +5emc_A    
                                       !  
  ----EC--KA--RGRG--------------   L   +-------------------4nqa_I    
                                     


> 1dh3_C:CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING

  
  ----------RG------NC----YGAT----RC   L     +------4eot_A    
                                             ! 
  --RC------NC----AAAT----CTRC------   L   +-5      +2wt7_A    
                                           ! !  +---1 
  --RG------NC----YGAT----CTRG------   L   ! !  !   +2wt7_B    
                                           ! +--4 
  ----------------NTRT--ATAT--CTRA--   L   !    ! +--5vpe_D    
                                         --6    +-3 
  RA--NA----AAVT----STRG------------   L   !      !  +1nwq_C    
                                           !      +--2 
  RG--QGNART--AGQT----FTRG----------   L   !         +1gd2_G    
                                           ! 
  ----------NCTT----AT------RG------   L   +--------2dgc_A    
                                         


> 1dsz_A:STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1

  
  ----EA--KG--RTRTRT--                              +-2han_B    
                                                  +-7 
  ----EC--KG--RGRG----   L                        ! +-2nll_B    
                                               +-12  
  CA--EC--KG--KGRG----   L                     !  !  +--1cit_A    
                                               !  +-10  
  ----EA--KG--RTRG----   L                     !     +--1kb2_B    
                                            +-14  
  ----EC--KG--KGRA----   L                  !  !     +5l0m_A    
                                            !  !  +--2 
  ----EC--KG--KGRG----   L                  !  !  !  +2ff0_A    
                                            !  +-13  
  ----DG--KG--RTRG----   L               +-15     !   +3cbb_A    
                                         !  !     ! +-1 
  --HGECAGKGAAKGRT----   L               !  !     +-9 +1lo1_A    
                                         !  !       ! 
  ----EC--KG--KGRG----   L               !  !       +-1dsz_B    
                                         !  !  
  --HAEC--KG--RGRG----   L               !  +----1a6y_A    
                                         !  
  --------KGVG------RA   L   +----------16        +3g6t_A    
                             !           !      +-3 
  --HC----KGVT--RG--RT       !           !      ! +3g9m_B    
                             !           !    +-8 
  --------KGVT--RG----   L   !           !    ! !   +2c7a_B    
                             !           !    ! ! +-4 
  --------KGVT--RG----   L   !           !    ! +-6 +5cbz_E    
                           -17           +---11   ! 
  --------KAVA--RA----   L   !                !   +5e69_A    
                             !                !  
  ----ET--KGAT--RG----   L   !                ! +1lat_A    
                             !                +-5 
  --------KGVT--RG----       !                  +5emc_A    
                             !  
  ----EC--KA--RGRG----   L   +-------------------4nqa_I    
                           


> 1dsz_B:STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1

  
  ----EC--KG--KGRG----   L               +1dsz_B    
                             +-----------8 
  ----EC--KA--RGRG----   L   !           +4nqa_I    
                             !  
  ----EA--KG--RTRTRT--       !            +-2han_B    
                             !        +--11  
  ----EC--KG--RGRG----   L   !        !   +-2nll_B    
                             !        !  
  --------KGVT--RG----   L   !        !         +5cbz_E    
                             !        !       +-5 
  --------KGVT--RG----   L   !        !       ! +2c7a_B    
                             !     +-14     +-9 
  --------KAVA--RA----   L   !     !  !     ! ! +5e69_A    
                           -17     !  !     ! +-7 
  ----ET--KGAT--RG----   L   !     !  !  +-12   ! +1lat_A    
                             !     !  !  !  !   +-3 
  --HC----KGVT--RG----       !     !  !  !  !     +3g9m_B    
                             !     !  !  !  !  
  --------KGVT--RG----       !     !  +-13  +-5emc_A    
                             !  +-15     !  
  ----DG--KG--RTRG----   L   !  !  !     !   +3cbb_A    
                             !  !  !     ! +-2 
  ----EA--KG--RTRG----   L   !  !  !     +-4 +1kb2_B    
                             !  !  !       ! 
  CA--EC--KG--KGRG----   L   !  !  !       +1cit_A    
                             !  !  !  
  --HGECAGKGAAKGRT----   L   +-16  !     +1lo1_A    
                                !  +----10  
  ----EC--KG--KGRA----   L      !        ! +5l0m_A    
                                !        +-1 
  ----EC--KG--KGRG----   L      !          +2ff0_A    
                                !  
  --------KGVG--RG--RA   L      !        +3g6t_A    
                                +--------6 
  --HAEC--KG--RGRG----   L               +1a6y_A    
                           


> 1dux_F:ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA- BINDING SURFACE AFFECT DNA-RECOGNITION

  
  ----------DCKT--RG----RGYA----------------   L                              +1dux_F    
                                                                           +--1 
  ------------KT--RGAT--RGYT----------------   L                           !  +1awc_A    
                                                                   +-------6 
  ------------KT--RGAT--RGYA----------------   L                   !       ! +--1bc8_C    
                                                                   !       +-5 
  ------------KT--RGSA--RGQA----------RA----   L              +----8         +--1yo5_C    
                                                              !    ! 
  ------------ST--------RTQT--MT------------   L              !    !          +5d8k_B    
                                                      +-------9    +----------2 
  --KTHG------------------------------------          !       !               +5hdn_C    
                                                      !       ! 
  ----------KG----ATNT--CT----SC------------   L      !       !              +-2irf_L    
                                                      !       +--------------3 
  ------------------NT--CT--NGST------------   L      !                      +-1if1_B    
                                                   +-12  
  TT--------KATTQTTG----LTRT----KA------FTYT   L   !  !                       +-2p7c_B    
                                                   !  !                  +----4 
  ----------KGTA--TA------RG----------------   L   !  !      +-----------7    +-1xsd_A    
                                                   !  !      !           ! 
  --------------------RAHT--STLT------------   L -13  !  +--10           +------2a07_K    
                                                   !  !  !   !  
  ----------RGRGYC--------------------------   L   !  +-11   +------------------1cf7_A    
                                                   !     !  
  --------------------------------KGKG------   L   !     +----------------------5xfr_B    
                                                   !  
  ------ITRGECSCSGKG------------------------   L   +---------------------------5i2d_R    
                                                 


> 1e3o_C:CRYSTAL STRUCTURE OF OCT-1 POU DIMER BOUND TO MORE



> 1efa_B:CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF

  
  LTYCSGYGQC--STRG--HT--AGLGAC   L     +1efa_B    
                                     +-2 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   ! ! +3oqm_C    
                                   --3 +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L   !   +1rzr_C    
                                     ! 
  ----SG--TC------RG------LCKA   L   +1qpz_A    
                                   


> 1emh_A:CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA

  
  --------PTLA----------                            +1emh_A    
                                                  +-1 
  --------PALA----------                       +--2 +4uqm_A    
                                               !  ! 
  --------PTLT----------       +---------------3  +-5nnu_A    
                               !               ! 
  KT----TT------RA------     --5               +----4yig_E    
                               ! 
  ----RA--RCQTNT--QGTCRC   L   !      +-------------2dp6_A    
                               +------4 
  VGRG----------PG------              +-------------1oe4_B    
                             


> 1ewq_A:CRYSTAL STRUCTURE TAQ MUTS COMPLEXED WITH A HETERODUPLEX DNA AT 2.2 A RESOLUTION

  
  ----FGET----------                                  +--1ewq_A    
                                                    +-1 
  MGDAFGTTRCMC--PT--   L                          +-2 +--1wb9_A    
                                                  ! ! 
  --YGKA------SAPA--                           +--3 +----3thx_B    
                                               !  ! 
  VCKCFGET------PG--       +-------------------4  +-----2o8b_B    
                           !                   ! 
  --DGFG------VGSG--     --5                   +--------3thx_A    
                           ! 
  ----------------RT       +----------------------------1jfi_B    
                         


> 1eyg_D:CRYSTAL STRUCTURE OF CHYMOTRYPTIC FRAGMENT OF E. COLI SSB BOUND TO TWO 35-MER SINGLE STRAND DNAS

  
  --RCVC----NC------RC----------VCNCTCACSCECWC----TCECWCRC----FC--KCECVCECYC--------QC------RC--------------NCVC--TCQC   L                            +1eyg_D    
                                                                                                                                                   +--1 
  ET--------RTCT----KT--LTNT----VTTTSTATNTETWT--KTTTDTWTRT--YT------------YT----RT------HT--RTKT--WTQTITETITST--------   L              +----------2  +3ulp_D    
                                                                                                                                        !          ! 
  --RT------NTDT--------------------STATNT----QT--TT--WT--------------------------------------------------------------       +----------3          +---5odn_B    
                                                                                                                             !          ! 
  ------NT----------RT------MT--VTET--------------------RTST--LT--------------------TT--ETYTRTQT----------------------   L   !          +--------------3udg_C    
                                                                                                                           --6 
  --------YT--------------------------------------------------YGDG----------------ST--HT----------------------YTRT----   L   !      +------------------3kjp_A    
                                                                                                                             !   +--4 
  ------------DGTGFGYGKT------YT----KG--------------------------------FG----IGHG--------------------------------------   L   +---5  +------------------2i0q_A    
                                                                                                                                 ! 
  ----------------RTWT----------------------------------------FTNT--------------------RT--------KT--------------------   L       +---------------------4gnx_Z    
                                                                                                                           


> 1f2i_J:COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA

  
  ----HCHGRG--TA--ACNA--KGRG   L       +--------------1tf6_A    
                                     +-6 
  ----ECYC----NTYGQGFT------   L     ! !     +--------5vmy_A    
                                     ! +-----5 
  QA--TTNA--STQAQTATSTNTAT--   L   +-7       !       +1g2f_F    
                                   ! !       +-------2 
  RGSTDAHARG--RGSTDCHG--TT--   L   ! !               +5kl3_A    
                                   ! ! 
  RG--DGECRG--RGSGDCHA------   L --8 +---------------2wbs_A    
                                   ! 
  RG--DAQARG--RGSTDCHG--TT--   L   !              +-6b0o_A    
                                   !            +-3 
  --TCYCKARG--QA----TC------   L   !            ! +-5yeg_A    
                                   +------------4 
  QA--ATHG----RG--DCNA--TT--   L                !   +2i13_A    
                                                +---1 
  RG----ET----RG--SCEC--RG--   L                    +5v3j_F    
                                 


> 1f4k_B:CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B- SITE DNA COMPLEX

  
  ----------TT--RGRT------------------SG----RT----KT----   L                                 +--2v1u_A    
                                                                    +------------------------2 
  ----------ST--RG----------------------NGRA------VG----   L        !                        +--2qby_B    
                                                                    ! 
  ----TT--------KATTQTTG--LTRT----KA----------------FTYT   L        !                       +-----2p7c_B    
                                                                    !                     +-3 
  ------------------NA--RAHT--STLT----------------------   L        !             +-------4 +-----2a07_K    
                                                                  +-9             !       ! 
  ------YC--KTHGSTQTYTPT--------------------LG----------   L      ! !           +-6       +------5x11_A    
                                                                  ! !           ! ! 
  KAFA--------------------------------------------------          ! ! +---------7 +--------------3aaf_B    
                                                                  ! ! !         ! 
  ------------------NASTRTHT--ST------------------------   L      ! ! !         !      +---------3l2c_A    
                                                               +-10 ! !         +------5 
  --------SG--YCNC--------------------------------------       !  ! +-8                !      +--2ve9_C    
                                                               !  !   !                +------1 
  ------------------------YG----------------------------       !  !   !                       +--4lb5_B    
                                                             -11  !   ! 
  ----------------------------------RG------------YG----   L   !  !   +--------------------------5vfx_A    
                                                               !  !  
  ----------STQTPTPGTTRG--------------------------------   L   !  +-----------------------------5xxp_A    
                                                               !  
  ----------DCKGRG----NARTKT------------------KGRA------   L   +-----------------------------5ddg_A    
                                                             


> 1f5t_A:DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

  
  --------------ST--PTTC--QG------RG--------------   L                         +-----------1f5t_A    
                                                                            +-14  
  --------------STPTATATTTKG----------------------   L                      !  +-----------5yi2_J    
                                                                        +--15  
  ----------------RGSTRTSTHG----------------------   L                  !   !       +----3zpl_B    
                                                                        !   !       !  
  --------------TT--PTTCSTNT----------------------   L                  !   +------10     +4lln_I    
                                                                        !           !   +-5 
  --------------DCSA--TATT--------RT--------------   L                  !           !   ! ! +1z9c_A    
                                                                    +--18           +---7 +-4 
  --------------LTRTPTNAVT--------------RT--------   L              !   !               !   +6c2s_D    
                                                                    !   !               ! 
  ----------------RGTCTA--RGNT--------------------   L              !   !               +4fx4_B    
                                                                    !   !  
  --------------STQTPTPGTTRG--------------HT------   L              !   !       +--------5xxp_A    
                                                                    !   +------13  
  ------------------QC----------------------------               +-19           +--------5hso_A    
                                                                 !  !  
  ------------------RGRGYC------------------------   L           !  !                    +1cf7_A    
                                                                 !  !    +---------------3 
  TTQT--------------------------------------------   L           !  !    !               +3gpl_A    
                                                                 !  !    !  
  --------TT--------KATTQTTG----LTRT--KA------FTYT   L           !  !    !            +---2p7c_B    
                                                                 !  !    !         +--9 
  --------------STQASGATSTQT----------------QA----   L           !  +---17  +-----12  +---4on0_B    
                                                                 !       !  !      !  
  --------------STKTPTTTFT--------------RA--------   L           !       !  !      +------4aso_F    
                                                                 !       !  !  
  ------------------------------YG----------------           +--20       !  !               +2heo_D    
                                                             !   !       +-16             +-1 
  ------------------------------YGRG--------------           !   !          !          +--6 +4wcg_B    
                                                             !   !          !          !  ! 
  ----------SGQG--YCNC----------------------------           !   !          !       +--8  +2ve9_C    
                                                             !   !          !       !  ! 
  ------------------------------YG----------------           !   !          !       !  !  +4ka4_B    
                                                         +--21   !          +------11  +--2 
  ------------------KGTA--TA------RG--------------   L   !   !   !                  !     +1xsd_A    
                                                         !   !   !                  !  
  ----------RG--STRGMCTTRT------------------------   L   !   !   !                  +-----4u0y_B    
                                                       -22   !   !  
  --------ST----STQAQGSTSART----------------------   L   !   !   +--------------------5trd_B    
                                                         !   !  
  ----KAFA------------------------------FGMC------       !   +------------------------3aaf_B    
                                                         !  
  ------------------SAQT------RGQT--NG------QT----   L   +----------------------------3wgi_D    
                                                       


> 1fiu_C:TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA

  
  DCSC------QC--------RGSGDCRGRG   L           +-------------------1fiu_C    
                                       +-------2 
  ----NGACKG------RCSGRGSADCRG--   L   !       !           +-------3dvo_D    
                                     --3       +-----------1 
  ------------SCNG--SGRG----RG--   L   !                   +-------3v1z_B    
                                       ! 
  ------------VCRC----AAEARG----   L   +---------------------------5dwa_A    
                                     


> 1fjl_B:HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE



> 1flo_A:FLP RECOMBINASE-HOLLIDAY JUNCTION COMPLEX I

  
  --AATAYGTTKGRAFCKC--KC----NT--RGSTKT--   L   +---------------------1flo_A    
                                             --3 
  LTNTTT----------------TTQAATYGYAKT----   L   !      +--------------5jk0_B    
                                               +------2 
  ------------------KA--SA------QG----RA   L          !   +----------5u91_B    
                                                      +---1 
  --------------------------------RC----   L              +----------6en1_A    
                                             


> 1fok_A:STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA



> 1g2d_F:STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (CLONE #2)

  
  --KT--STHT----RG--DAQA--RGRGSTDCHGTT--   L                   +-6b0o_A    
                                               +---------------3 
  ITST--STHTRG--RG----EA--RA--TTTGECRG--   L   !               +-5v3j_F    
                                               ! 
  --QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L   !                  +1g2f_F    
                                               !          +-------1 
  --KG--WTKA--------HCHG--RGTA--ACNAKGRG   L   !          !       +1tf6_A    
                                             --8       +--5 
  --RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L   !       !  !       +-5kl3_A    
                                               !       !  ! +-----2 
  --EC--SCKGRG----TCYCKA--RGQA----TC----   L   ! +-----6  +-4     +-5yeg_A    
                                               ! !     !    ! 
  ------TTSGRG------ECYC----NTYGQGFT----   L   ! !     !    +-------5vmy_A    
                                               +-7     ! 
  --QARGATNA----QA--ATHG----RG--DCNATT--   L     !     +----------2i13_A    
                                                 ! 
  --------------RG--DGEC--RGRGSGDCHA----   L     +----------------2wbs_A    
                                             


> 1g2f_F:STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6)

  
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L                     +1g2f_F    
                                                             +-1 
  KT--STHT----RG--DAQA--RGRGSTDCHGTT--   L                   ! +6b0o_A    
                                                     +-------3 
  QARGATNA----QA--ATHG----RG--DCNATT--   L           !       ! +2i13_A    
                                                     !       +-2 
  ----STQTLTITST--STHT--RGRG----EARA--   L     +-----6         +5v3j_F    
                                               !     ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L     !     !       +-5kl3_A    
                                               !     ! +-----4 
  EC--SCKGRG----TCYCKA--RGQA----TC----   L   +-7     +-5     +-5yeg_A    
                                             ! !       ! 
  ----TTSGRG------ECYC----NTYGQGFT----   L   ! !       +-------5vmy_A    
                                           --8 ! 
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L   ! +---------------1tf6_A    
                                             ! 
  ------------RG--DGEC--RGRGSGDCHA----   L   +-----------------2wbs_A    
                                           


> 1gcc_A:SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

  
  RGRG------EC--RG------RGWC--   L   +------------------------5wx9_A    
                                     ! 
  RGRG--WA--EC--RG------RGWC--   L --3                  +-----1gcc_A    
                                     !     +------------1 
  ----RT--------------------QG   L   +-----2            +-----5d3g_A    
                                           ! 
  --KA----YT--KG--RGECSARG----   L         +------------------3rmp_A    
                                   


> 1gd2_G:CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA

  
  --------------RG------NC----YGAT--CTRG   L     +------2wt7_B    
                                                 ! 
  RGQGNART--AGQT----FTRG----------------   L   +-5     +1gd2_G    
                                               ! !     ! 
  RC--NC----AAAT----CTRC----------------   L   ! !     !     +2wt7_A    
                                               ! +-----4   +-1 
  ----NTRT--ATAT----CTRA----------------   L   !       ! +-2 +5vpe_D    
                                             --6       ! ! ! 
  --------RG------NC----YGAT------RC----   L   !       +-3 +4eot_A    
                                               !         ! 
  ------RA----NA----AAVT----STRG--------   L   !         +1nwq_C    
                                               ! 
  ----NCTT----AT------RG----------------   L   +--------2dgc_A    
                                             


> 1gji_A:CRYSTAL STRUCTURE OF C-REL BOUND TO DNA

  
  RGRGYTCTEC--------RT------   L                               +1gji_A    
                                                             +-1 
  RGRGYTCTEC--SG----RT------   L                         +---2 +2i9t_A    
                                                         !   ! 
  RGRGYTCTECRG------KT------   L   +---------------------4   +3do7_A    
                                   !                     ! 
  RGRGYTCCEC------KTKTPTKTRG   L   !                     ! +--1nfk_A    
                                 --5                     +-3 
  RGRGYTCCEC----HG--KG------   L   !                       +--1a3q_A    
                                   ! 
  RGRG----EGRG--------------   L   +-------------------------1bvo_A    
                                 


> 1gm5_A:STRUCTURE OF RECG BOUND TO THREE-WAY DNA JUNCTION

  
  KAFAMGIA--KA--FGNCQCYG----------EA--NG--------            +-----------------------1gm5_A    
                                                         +--2 
  ------------------------------------------NALA   L     !  +-----------------------3v4r_B    
                                                       +-4 
  --------------------------------------VC------       ! ! +------------------------2wwy_B    
                                                       ! +-3 
  ----------------------------------------RT----   L --5   !                +-------5vvr_M    
                                                       !   +----------------1 
  ----------------------------------------RG----       !                    +-------6ftx_W    
                                                       ! 
  --------RT--IG--WGDG--KGDTHTLTYAEGIG----------   L   +----------------------------4hja_A    
                                                     


> 1gt0_C:CRYSTAL STRUCTURE OF A POU/HMG/DNA TERNARY COMPLEX



> 1gt0_D:CRYSTAL STRUCTURE OF A POU/HMG/DNA TERNARY COMPLEX

  
  KCNT--MAMA--EGSAACNT--YT   L      +----2lef_A    
                                    ! 
  RTNTFTMA--RT--NG--SAYA--   L   +--3   +4y60_C    
                                 !  ! +-1 
  RCNTFTMA--RAHGNT--SAYA--   L   !  +-2 +3f27_D    
                               --4    ! 
  --STYGLASGLA--TGTCIT----   L   !    +--3tq6_B    
                                 ! 
  ----FTIA--RT--QTLAMT----   L   +-------5jh0_D    
                               


> 1gxp_A:PHOB EFFECTOR DOMAIN IN COMPLEX WITH PHO BOX DNA.

  
  ------------NTVC--ECSTYT--STYC------RA----   L                +---------------------5ed4_A    
                                                                ! 
  ------------RG----DTVT----ST--RG----RC----   L                !       +-------------4nhj_A    
                                                                !     +-7 
  --------------------------------YG--------                +---9     ! !            +4lb5_B    
                                                            !   !     ! +------------2 
  TT----------KATT--QTTG----------LTRT--FTYT   L            !   !     !              +2p7c_B    
                                                            !   !     ! 
  ------------RGRG--YC----------------------   L            !   +-----8            +---1cf7_A    
                                                            !         !            ! 
  --------------------------------YG--------                !         !          +-5    +4ka4_B    
                                                            !         !          ! !  +-3 
  ----SGQG--YCNC----------------------------             +-12         !          ! !  ! +2ve9_C    
                                                         !  !         !          ! +--4 
  --------------------------------YG--------             !  !         +----------6    ! +2heo_D    
                                                         !  !                    !    +-1 
  ----------------------------------RG------             !  !                    !      +4wcg_B    
                                                         !  !                    ! 
  --RG----STRGMCTT--RT----------------------   L      +-13  !                    +----4u0y_B    
                                                      !  !  !  
  ------------KGTC--KGTCHT------------------   L      !  !  +-------------------------4wuh_B    
                                                      !  !  
  --------------HT----RTITYT----------------   L      !  !      +---------------------4kfc_B    
                                                   +-14  !  +--10  
  LTET----TTRAECRC--RCQC--------------------   L   !  !  +-11   +---------------------3n97_A    
                                                   !  !     !  
  ----------RCET------SA----QAKG------------   L -15  !     +-------------------------5lxu_A    
                                                   !  !  
  --------------RGAC----LG------------------       !  +-----------------------------4wx9_A    
                                                   !  
  YG------------TG--RGSG----FTRG------------   L   +-----------------------------2h27_A    
                                                 


> 1h6f_B:HUMAN TBX3, A TRANSCRIPTION FACTOR RESPONSIBLE FOR ULNAR-MAMMARY SYNDROME, BOUND TO A PALINDROMIC DNA SITE

  
  RGTTATFT--FG   L       +1h6f_B    
                       +-1 
  RGTTATFTACFG   L   +-2 +6f59_B    
                     ! ! 
  RGTT--FG--FT     --3 +-5t1j_B    
                     ! 
  RGTTATFG--FG       +-4a04_B    
                   


> 1h89_C:CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2

  
  ------KG--RTEC----NAKGNANTST   L                    +---1h89_C    
                                     +----------------2 
  --NA--RTQT--EC----NG--NA----   L   !                !  +2kdz_A    
                                   --3                +--1 
  ------KG--RAEA--DCNAKGNANTST   L   !                   +3zqc_A    
                                     ! 
  RT--STVC--KGDCRG------------   L   +--------------------1w0t_A    
                                   


> 1h8a_C:CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3

  
  ------KG--RTEC----NAKGNANTST   L                    +---1h89_C    
                                     +----------------2 
  ------KG--RAEA--DCNAKGNANTST   L   !                ! +--3zqc_A    
                                   --3                +-1 
  --NA--RTQT--EC----NG--NA----   L   !                  +--2kdz_A    
                                     ! 
  RT--STVC--KGDCRG------------   L   +--------------------1w0t_A    
                                   


> 1h9t_B:FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR

  
  RG--TGRGTG--RTET------HA------   L                      +--1h9t_B    
                                       +------------------5 
  RG--TTRGTTTTRTET------HA------   L   !                  +--4p9u_B    
                                       !  
  RG--STRGMCTTRT----------------   L   !          +----------4u0y_B    
                                       !          ! 
  SGQG--YCNC--------------------       !          !           +2ve9_C    
                                     -10       +--8         +-2 
  --------KATTQTTGLTRTKA----FTYT   L   !       !  !   +-----4 +2p7c_B    
                                       !       !  !   !     ! 
  ----------------YG------------       !       !  !   !     +4lb5_B    
                                       !       !  +---7 
  --------RGRGYC----------------   L   !       !      !  +---1cf7_A    
                                       +-------9      +--6 
  ----------------YGRG----------               !         !  +4wcg_B    
                                               !         +--3 
  ----------------YG------------               !            ! +2heo_D    
                                               !            +-1 
  ----------------YG------------               !              +4ka4_B    
                                               ! 
  ----STKTPTTTFT----------RA----   L           +-------------4aso_F    
                                     


> 1hcq_E:THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS

  
  ----EA--KG--RTRTRT                +-2han_B    
                                 +-11  
  ----EC--KG--KGRG--   L         !  ! +1dsz_B    
                                 !  +-9 
  --HGECAGKGAAKGRT--   L      +-15    +1lo1_A    
                              !  !  
  --------KAVA--RA--   L      !  !  +5e69_A    
                              !  +--1 
  ----EC--KG--RGRG--   L   +-16     +2nll_B    
                           !  !  
  ----ET--KGAT--RG--   L   !  !    +1lat_A    
                           !  !  +-2 
  --------KGVT--RG--   L   !  +--3 +2c7a_B    
                           !     ! 
  ----EC--KA--RGRG--   L   !     +4nqa_I    
                           !  
  --------KGVG--RG--   L -17         +3g6t_A    
                           !       +-5 
  ----EC--KG--KGRG--   L   !     +-7 +2ff0_A    
                           !     ! ! 
  --------KGVT--RG--   L   !  +-12 +5cbz_E    
                           !  !  !  
  --------KGVT--RG--       !  !  ! +5emc_A    
                           !  !  +-4 
  ----EC--KG--KGRA--   L   !  !    +5l0m_A    
                           +-14  
  --HAEC--KG--RGRG--   L      !     +1a6y_A    
                              !  +-10  
  ----EA--KG--RTRG--   L      !  !  ! +1kb2_B    
                              !  !  +-6 
  CA--EC--KG--KGRG--   L      +-13    +1cit_A    
                                 !  
  --HC----KGVT--RG--             ! +3g9m_B    
                                 +-8 
  ----DG--KG--RTRG--   L           +3cbb_A    
                         


> 1hlo_B:THE CRYSTAL STRUCTURE OF AN INTACT HUMAN MAX-DNA COMPLEX: NEW INSIGHTS INTO MECHANISMS OF TRANSCRIPTIONAL CONTROL

  
  KT----HGNT----EC--RCRG   L                      +1nkp_A    
                                               +--1 
  ------HGNT--LGEC--RCRC   L                   !  +5i50_B    
                                             +-6 
  ------HGNT--LCEC--RCRG   L                 ! ! +1hlo_B    
                                             ! +-2 
  ------HGNT--IAEC--YCRG   L               +-8   +1am9_A    
                                           ! ! 
  ----HGNT--IAEC--RCRT--   L               ! ! +--4ati_B    
                                           ! +-5 
  ------HGNT--MTEA--RCRG   L   +-----------9   ! +1nlw_D    
                               !           !   +-4 
  ------HGNT----EC--RCRG   L   !           !     +1nkp_E    
                               !           ! 
  --RT----NT--RGEC--RCQT       !           +------2ypa_A    
                               !  
  ------RTNT----EC--RCRG   L -13           +-------4h10_B    
                               !     +----10  
  ----QG------VTEC--RCRG   L   !     !     +-------1an4_A    
                               !  +-11  
  --RG----TT--RAEC--RC--       !  !  !         +---1mdy_C    
                               !  !  +---------7 
  ------HGST--ITET--RCRG   L   +-12            !  +4h10_A    
                                  !            +--3 
  ------HG----ITEC--RCRG   L      !               +5nj8_D    
                                  !  
  ------HG------ET--RTRG   L      +---------------5v0l_A    
                             


> 1ic8_B:HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT

  
  NTQASAHT--STQT----TTPGRTYCNAATNAKG--   L                             +-1ic8_B    
                                                     +-----------------1 
  NTQASTHT--STQT----TT--RAYT----NAKG--   L       +---2                 +-2h8r_B    
                                                 !   ! 
  STQATT----------RG----RARCVTCTNAQTRC   L   +---3   +-------------------1au7_A    
                                             !   ! 
  TTQA--LT--SAET----------------------   L --4   +-----------------------2o4a_A    
                                             ! 
  ST--SCATRT--NCQT--HT----------------   L   +---------------------------4jcy_A    
                                           


> 1if1_B:INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA

  
  HC------NT--RGCT--NGST   L                         +1if1_B    
                                                   +-1 
  --KG--ATNT--RTCT----SC   L         +-------------3 +2irf_L    
                                     !             ! 
  --------------------RG             !             +-4hly_B    
                                     ! 
  ----KTRGAT----RGYA----   L   +-----7             +-1bc8_C    
                               !     !          +--4 
  ----KTRGSA----RGQA----   L   !     !          !  ! +1yo5_C    
                               !     +----------5  +-2 
  --DCKTRG------RGYA----   L --8                !    +1dux_F    
                               !                ! 
  ----KT--RGAT--RGYT----   L   !                +----1awc_A    
                               ! 
  ------NA----RAHT--STLT   L   !               +-----2a07_K    
                               +---------------6 
  ------NAST--RTHT--ST--   L                   +-----3l2c_A    
                             


> 1ig7_A:MSX-1 HOMEODOMAIN/DNA COMPLEX STRUCTURE



> 1ign_A:DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE

  
  ----HG--NCSCRGHCRG--YC----KANA--RGDC--RGKT----TCTCPTNC   L      +-------------------1ign_A    
                                                               +-10  
  --------------NCICNA--RGRG----------------------------   L   !  +-------------------6fqp_B    
                                                               !  
  --------------NCITNA--RGRG----------------------------   L   !                     +6fqq_E    
                                                               !       +-------------2 
  ----------------KGNA----------------------------------   L   !       !             +2hos_A    
                                                               !       ! 
  ------------RTVAIANA--MCRG----------------------------   L -11       !                 +1le8_A    
                                                               !       !               +-1 
  HTRT----------NCSTNA--RG------------------------------   L   !     +-8             +-3 +1k61_B    
                                                               !     ! !             ! ! 
  RT------------NT--NA--IARG----------------------------   L   !     ! !           +-5 +4cyc_B    
                                                               !     ! !           ! ! 
  --------------IAKGNA----------------------------------   L   !     ! !        +--6 +2hdd_A    
                                                               +-----9 !        !  ! 
  ------RCET----SAQAKG----------------------------------   L         ! +--------7  +-5lxu_A    
                                                                     !          ! 
  --------------------------RT--NT----NA----IARG--------   L         !          +----1puf_B    
                                                                     ! 
  --------------ITQTNA----RG----------------------------   L         !             +6dfy_D    
                                                                     +-------------4 
  ------STVC--KGDCRG------------------------------------   L                       +1w0t_A    
                                                             


> 1imh_C:TONEBP/DNA COMPLEX

  
  RG--YTTTECRG--QA--   L   +---------------1imh_C    
                           ! 
  RGRGYTCC--HTKT--RG   L --3             +--1nfk_A    
                           !           +-1 
  RGRGYTEC--HG------   L   +-----------2 +--1a3q_A    
                                       ! 
  RGRGYTEC----------   L               +---1gji_A    
                         


> 1j1v_A:CRYSTAL STRUCTURE OF DNAA DOMAINIV COMPLEXED WITH DNAABOX DNA

  
  RALTPTDCHGTCTCLTHT----------   L               +-------------1j1v_A    
                                     +-----------3 
  ----------------NT----NAIARG   L   !           !       +-----1puf_B    
                                     !           +-------2 
  --------RCET----SA--QAKG----   L --4                   !   +-5lxu_A    
                                     !                   +---1 
  ----------------NT----NAIARG   L   !                       +-4cyc_B    
                                     ! 
  ----------KGTCKGTCHT--------   L   +-------------------------4wuh_B    
                                   


> 1j47_A:3D SOLUTION NMR STRUCTURE OF THE M9I MUTANT OF THE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA

  
  --RC--NAFTIA--RG--NC----SALT------YAKTEAKA   L   +----------------------2gzk_A    
                                                   !  
  --RC--NTFTMA--RA--NGSC--ST--------YA--RG--   L   !                       +1gt0_D    
                                                   !                     +-1 
  --KC--NT--MAMA--EGSAAC--NT------------YT--   L   !           +---------4 +2lef_A    
                                                 -10           !         ! 
  --RT--NTFTMA--RT--NG----SA--------YA------   L   !     +-----8         +4y60_C    
                                                   !     !     ! 
  --RT--NTFTMA--RA--NGAC--ST--------YA------   L   !     !     !         +4s2q_D    
                                                   !     !     +---------5 
  --RC--NTFTMA--RAHGNT----SA--------YA------   L   !     !               +3f27_D    
                                                   +-----9 
  --RC--NTFTMA--RAHTNTAT--SA--------YA------   L         !              +-3u2b_C    
                                                         !       +------6 
  ------------VT----FG--FCSA----------------             !       !      ! +4qr9_A    
                                                         !       !      +-2 
  ------STYGLASGLA--TGTC--IT----------------   L         +-------7        +3tq6_B    
                                                                 ! 
  KCRC----YTMALTRA--VCTG--AA----VCEC--------   L                 !        +1qrv_A    
                                                                 +--------3 
  --RTTASTYAFALT----PTAT--ST--RA------------   L                          +5jh0_D    
                                                 


> 1j5n_A:SOLUTION STRUCTURE OF THE NON-SEQUENCE-SPECIFIC HMGB PROTEIN NHP6A IN COMPLEX WITH SRY DNA

  
  VGTTRTTGRTRT--SAYCMT------FT------   L           +-----1j5n_A    
                                              +----3 
  ----------RTTASTYAFALT----PTATSTRA   L   +--4    +-----5jh0_D    
                                           !  ! 
  --------------STYGLASGLA--TGTCIT--   L   !  +----------3tq6_B    
                                         --5 
  ----------RT--NTFTMA--RT--NG--SA--   L   !            +4y60_C    
                                           +------------2 
  ----------RC--NTFTMA--RAHGNT--SA--   L                ! +3f27_D    
                                                        +-1 
  ----------KC--NT--MAMA--EGSAACNT--   L                  +2lef_A    
                                         


> 1je8_F:TWO-COMPONENT RESPONSE REGULATOR NARL/DNA COMPLEX: DNA BENDING FOUND IN A HIGH AFFINITY SITE

  
  ------KGTC--KGTCHT--------   L                        +----4wuh_B    
                                       +----------------2 
  ----ITKGTA--STSAQT--------   L       !                +----5w43_B    
                                   +---6 
  TT----KATT----QTTG--LTRTYT   L   !   !                +----2p7c_B    
                                   !   !  +-------------3 
  --ST--RG------------------   L   !   +--5             +----2qby_B    
                                 --7      ! 
  --STQTPTPG--TTRG----------   L   !      +------------------5xxp_A    
                                   ! 
  --DCSA----TA--TT------RT--   L   !        +----------------1z9c_A    
                                   +--------4 
  ------------------YG------                !               +2heo_D    
                                            +---------------1 
  --------------------YG----                                +4ka4_B    
                                 


> 1jfi_A:CRYSTAL STRUCTURE OF THE NC2-TBP-DNA TERNARY COMPLEX



> 1jfi_B:CRYSTAL STRUCTURE OF THE NC2-TBP-DNA TERNARY COMPLEX



> 1jgg_B:EVEN-SKIPPED HOMEODOMAIN COMPLEXED TO AT-RICH DNA



> 1jj4_B:HUMAN PAPILLOMAVIRUS TYPE 18 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET

  
  ------------------------------------------------------------------------------------------WG--                +----------------------------6dgd_B    
                                                                                                                !  
  --DG--IC--LG----WG----------------------QG--KT----------KG--FGFG------------------------RG--PC   L            !                         +----4y0f_A    
                                                                                                             +-11      +------------------5 
  --TA--FC--SG--------------------------LAKA------------TGSG--VGFA------------------------------   L         !  !  +---9                  +----5tkz_B    
                                                                                                             !  !  !   ! 
  --------------------------------------------------------------------RG------------------------   L         !  +-10   +-----------------------3qfq_B    
                                                                                                             !     !  
  ----------------KTTG--YCNG--RT----------------------------------------------------------------   L         !     !        +------------------1b3t_A    
                                                                                                             !     +--------8 
  --------------------------VC--------RC------IC------------RC--------PA--NA--FAKC------KC------   L         !              +------------------3vke_A    
                                                                                                             !  
  EC------ST--KG--------------------------------TT--NA--------MG--SC----------------------------   L      +-12                               +5t2n_A    
                                                                                                          !  !                             +-1 
  ST------EC--TT------------------------------------RG----TT--RG--------------------------------   L      !  !                             ! +5thg_A    
                                                                                                          !  !                           +-3 
  ----RG--VT--SA--------------------------------FC--MC----ST--QT--EC----------------------------   L      !  !                           ! ! +5esp_A    
                                                                                                          !  !                     +-----4 +-2 
  QA------KT--TG----------------------------RA--ET--RG------AT--DT------------------------------   L      !  !                     !     !   +4lq0_A    
                                                                                                       +-13  !             +-------6     ! 
  QT--FA--QG--NG--------------------------------HC--SC----LA--QG--QA----------------------------   L   !  !  !             !       !     +-4yit_A    
                                                                                                       !  !  +-------------7       ! 
  TG--ET------EC------------------------------RG--RG------MA----RG--RG--------------------------   L   !  !                !       +-------3uvf_B    
                                                                                                     -14  !                ! 
  ------------IG--------------------------NA--RG----RGDT--IC----RG------------------------------   L   !  !                +---------------2fld_B    
                                                                                                       !  !  
  --------------KG----QG--RG----HTRTQT--------------------------------------------AATTRT--------       !  +-----------------------------5ond_B    
                                                                                                       !  
  --PI------------------------------------------------------------------PI--VI------------------       +-----------------------------2xhb_A    
                                                                                                     


> 1jt0_C:CRYSTAL STRUCTURE OF A COOPERATIVE QACR-DNA COMPLEX

  
  TG--SAKG--NTYTYT   L                 +---1jt0_C    
                                  +----5 
  --PTTCRG----YGHA   L          +-6    +---6c31_A    
                                ! ! 
  VTRGAT----QTHTHT   L          ! +--------5vl9_A    
                                ! 
  TA--STECAGATYTRG   L          !           +4gck_A    
                             +--7         +-1 
  VT--AGDT--TTYTLA   L       !  !       +-2 +5gpc_B    
                             !  !       ! ! 
  TA----ECAC--YCRA           !  !     +-3 +5haw_A    
                         +---8  !     ! ! 
  TA--AT----LCFGHA       !   !  +-----4 +--4i6z_B    
                         !   !        ! 
  --EC--KGQCTGYGRC   L --9   !        +---4jl3_B    
                         !   ! 
  ----SCKGSG--IGYC   L   !   +------------2yvh_A    
                         ! 
  ----TGKG----YCFA   L   +----------------4pxi_B    
                       


> 1k3x_A:CRYSTAL STRUCTURE OF A TRAPPED REACTION INTERMEDIATE OF THE DNA REPAIR ENZYME ENDONUCLEASE VIII WITH BROMINATED-DNA

  
  QALGYA------------------RG                       +-1k3x_A    
                                                 +-3 
  RA--------FT------------RA   L                 ! ! +3gpu_A    
                                          +------4 +-1 
  RGMG------FC------------RG   L          !      !   +3u6p_A    
                                      +---5      ! 
  --MG------RC--FCKGDGACQTRG   L      !   !      +-1k82_A    
                                      !   ! 
  --MG--ITRC--FG------HG--RG   L   +--6   +--------5itu_A    
                                   !  ! 
  RTMTET--RC--------------RT       !  !          +-4pd2_A    
                                 --7  +----------2 
  --LG----RC--FC------NG--RT   L   !             +-3vk8_B    
                                   ! 
  --MG------RG--FG--------RG       +---------------3twm_A    
                                 


> 1k4t_A:HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX

  
  --ECRA--YAMCKT--NT--KT----------NT                             +------1k4t_A    
                                                    +------------1 
  NT--RGMGYAMCKT--NC--KTDA----TT----   L      +-----2            +------2b9s_A    
                                              !     ! 
  --------------RG--------RG--------   L   +--3     +-------------------3m4a_A    
                                           !  ! 
  ------------------KA------RA------   L --4  +-------------------------5u91_B    
                                           ! 
  ------------------------------NT--       +----------------------------2b9s_B    
                                         


> 1k61_B:MATALPHA2 HOMEODOMAIN BOUND TO DNA



> 1k82_A:CRYSTAL STRUCTURE OF E.COLI FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FPG) COVALENTLY TRAPPED WITH DNA

  
  RA--MG----RCFCKGDGACQTRG   L                  +--1k82_A    
                                              +-3 
  --RTMTET--RCFA--------RT                    ! !  +4pd2_A    
                                         +----4 +--2 
  --QALGYA--------------RG               !    !    +1k3x_A    
                                       +-5    ! 
  ----LG--MTRCFC----NG--RT   L         ! !    +---3vk8_B    
                                       ! ! 
  ----MG--ITRCFG----HG--RG   L   +-----6 +--------5itu_A    
                                 !     ! 
  --RGMG----RCFC--------RG   L   !     !         +3u6p_A    
                               --7     +---------1 
  --RA------RGFT--------RA   L   !               +3gpu_A    
                                 ! 
  ----MG----RGFG--------RG       +---------------3twm_A    
                               


> 1kb2_B:CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT

  
  ------EA--KG--RTRG----------   L                                       +1kb2_B    
                                                                     +---1 
  ------EC--KG--RGRG--------KA   L                                   !   +2nll_B    
                                                                 +--15  
  ------EA--KG--RTRT--RT------                                   !   !     +-2han_B    
                                                                 !   !  +-12  
  ------EC--KA--RGRG----------   L                          +---19   +-14  +-4nqa_I    
                                                            !    !      !  
  CA----EC--KG--KGRG--------RT   L                          !    !      +--1cit_A    
                                                            !    !  
  --HG--ECAGKGAAKGRT------RT--   L                          !    +-------1lo1_A    
                                                            !  
  ------EC--KG----RA------PA--   L                          !              +5krb_G    
                                                            !         +----4 
  ------EC--KG--KGRG----RC----   L                          !         !    +2ff0_A    
                                                            !         !  
  ------EA--KG--KTRG----------   L                          !         !       +4cn3_D    
                                                 +---------20         !     +-2 
  ------EC--KG--KGRG----------   L               !          !      +-17  +--7 +1dsz_B    
                                                 !          !      !  !  !  ! 
  ------DG--KG--RTRG----------   L               !          !      !  !  !  +3cbb_A    
                                                 !          !      !  !  !  
  ------EA--KG--KTRG----------   L               !          !      !  !  !       +2han_A    
                                                 !          !      !  +-16     +-5 
  ------EC--KG--KGRA----RT----   L               !          !      !     !     ! +5l0m_A    
                                                 !          !      !     !  +-11  
  ----------KGVT--RG----------   L               !          !      !     !  !  ! +5cbz_E    
                                                 !          !      !     !  !  +-9 
  ----------KAVA--RA----------   L               !          +-----18     !  !    ! +5e69_A    
                                              +-21                 !     +-13    +-3 
  ----------KGVT--RG----------   L            !  !                 !        !      +2c7a_B    
                                              !  !                 !        !  
  ------ET--KGAT--RG----------   L            !  !                 !        ! +1lat_A    
                                              !  !                 !        +-8 
  ----------KGVT--RG----------                !  !                 !          +5emc_A    
                                              !  !                 !  
  ------EC--KG--RGRG----------   L         +-22  !                 !      +1dsz_A    
                                           !  !  !                 !    +-6 
  --HA--EC--KG--RGRG----------   L         !  !  !                 +---10 +1a6y_A    
                                           !  !  !                      !  
  --HC------KGVT--RG------RT--             !  !  !                      +3g9m_B    
                                        +-23  !  !  
  ------EC--KGAG--RG----------   L      !  !  !  +-----------------------4ond_A    
                                        !  !  !  
  ----------KGVG--RG----------   L   +-24  !  +--------------------------4tnt_B    
                                     !  !  !  
  ------EC--KGAGKGRG----------   L   !  !  +---------------------------1hcq_E    
                                   -25  !  
  ----YGEC--KGAGKGRG----------   L   !  +---------------------------4oln_B    
                                     !  
  ------EC--KG--RGRGRT--------   L   +----------------------------3e00_D    
                                   


> 1kln_A:DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX

  
  LCNGKGYGMG----RCFCEC--EG------SGHGVC----------------------------------------------                                    +--1kln_A    
                                                                                                                      +-1 
  ------------------------KT--YG------RGNGNGRC----YG--YAIGSCYC--NGRC--FG--------QAHG                                +-2 +--4yfu_D    
                                                                                                                    ! ! 
  ------------------------NAKA--------RG--NT----QC----YCMC------QC--NGPTYGATRT--QC--                              +-3 +----4x0q_B    
                                                                                                                  ! ! 
  ------------------------KC----------RGNGNG----TGFG--YGMG----RG------KASAEARANGQGHG   L                +---------4 +-----4bwj_A    
                                                                                                        !         ! 
  ------------------------KT----------RG------EGKGYGACYCAC----RC--------QTATRTNGQGHC   L       +--------5         +-----4xvk_A    
                                                                                               !        ! 
  --------------------------KT--------RTNG------------YA------------------------QA--       +---7        +---------------1x9m_A    
                                                                                           !   ! 
  ----------------------------------------------QG--TGYGVG--YT----------------------   L --8   +------------------------4boc_A    
                                                                                           ! 
  ----------DAKT------FA------------------------------------------------------------       !         +------------------3qex_A    
                                                                                           +---------6 
  --------YT--RG--------------------------------------------------------------------                 +------------------2xhb_A    
                                                                                         


> 1kx5_B:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION



> 1kx5_D:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION



> 1kx5_E:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION



> 1kx5_G:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION



> 1lat_A:GLUCOCORTICOID RECEPTOR MUTANT/DNA COMPLEX

  
  ----EA--KG--RTRTRT               +2han_B    
                              +---10  
  ----EC--KG--RGRG--   L      !    +2nll_B    
                              !  
  --------KGVT--RG--   L   +-16      +2c7a_B    
                           !  !  +---1 
  ----EC--KA--RGRG--   L   !  !  !   +4nqa_I    
                           !  +-14  
  ----EC--KG--KGRG--   L   !     !  +--2ff0_A    
                           !     +-13  
  --HGECAGKGAAKGRT--   L   !        ! +1lo1_A    
                           !        +-9 
  ----EC--KG--KGRA--   L   !          +5l0m_A    
                           !  
  --HC----KGVT--RG--     -17      +-3g9m_B    
                           !      !  
  ----ET--KGAT--RG--   L   !      !     +1lat_A    
                           !   +-11   +-3 
  --HAEC--KG--RGRG--   L   !   !  ! +-7 +1a6y_A    
                           !   !  ! ! ! 
  ----EA--KG--RTRG--   L   !   !  +-8 +1kb2_B    
                           !   !    ! 
  ----DG--KG--RTRG--   L   !   !    ! +3cbb_A    
                           !   !    +-4 
  CA--EC--KG--KGRG--   L   +--15      +1cit_A    
                               !  
  --------KAVA--RA--   L       !        +5e69_A    
                               !      +-2 
  --------KGVT--RG--   L       !    +-5 +5cbz_E    
                               !    ! ! 
  ----EC--KG--KGRG--   L       !  +-6 +1dsz_B    
                               !  ! ! 
  --------KGVG--RG--   L       +-12 +3g6t_A    
                                  !  
  --------KGVT--RG--              +--5emc_A    
                         


> 1le8_A:CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2-3A HETERODIMER BOUND TO DNA COMPLEX



> 1le8_B:CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2-3A HETERODIMER BOUND TO DNA COMPLEX



> 1llm_D:CRYSTAL STRUCTURE OF A ZIF23-GCN4 CHIMERA BOUND TO DNA

  
  ----QA--TTNA--STQAQTATSTNTAT   L                                 +1g2f_F    
                                                                 +-1 
  ----RG--DAQARG--RGSTDCHG--TT   L                   +-----------2 +6b0o_A    
                                                     !           ! 
  ------TCYCKARG--QA----TC----   L                 +-4           +-5yeg_A    
                                                   ! ! 
  --------TTSGRG------ECYC----   L                 ! !   +---------5vmy_A    
                                     +-------------5 +---3 
  ----RGSTDAHARG--RGSTDCHG--TT   L   !             !     +---------5kl3_A    
                                   --6             ! 
  ----RG--DGECRG--RGSGDCHA----   L   !             +---------------2wbs_A    
                                     ! 
  NTEC--RCRG------------------   L   +-----------------------------1nkp_A    
                                   


> 1lmb_4:REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX

  
  KGKG--ET--QASG----------NG   L                  +1lmb_4    
                                      +-----------1 
  KGKG------QASG----------NG   L      !           +1rio_A    
                                   +--4 
  ----QT--STNTVTATSTQTRTETTT   L   !  !          +2r1j_L    
                                   !  !   +------2 
  ----------SCATRTNCQT----HT   L --5  +---3      +4jcy_A    
                                   !      ! 
  ------AT--QAAT--SA--------       !      +-------4z5h_A    
                                   ! 
  --------TT----ATYTQTQT----   L   +--------------3qws_B    
                                 


> 1lo1_A:ESTROGEN RELATED RECEPTOR 2 DNA BINDING DOMAIN IN COMPLEX WITH DNA

  
  --HGECAGKGAAKGRT------RT--RC   L             +1lo1_A    
                                          +----9 
  ----EC--KG--KGRA------RT--RC   L        !    ! +5l0m_A    
                                     +---16    +-1 
  ----EC--KG--KGRG------RC--RC   L   !    !      +2ff0_A    
                                     !    !  
  ----EC--KA--RGRG------------   L   !    +-----4nqa_I    
                                     !  
  CA--EC--KG--KGRG----RT--RT--   L   !        +--1cit_A    
                                     !        !  
  ----EA--KG--RTRTRT----------       !     +-13     +2han_B    
                                   -17     !  !  +-10  
  ----EA--KG--RTRG------------   L   !     !  !  !  ! +1kb2_B    
                                     !     !  +-12  +-2 
  ----EC--KG--RGRG------------   L   !     !     !    +2nll_B    
                                     !     !     !  
  ----EC--KG--KGRG------------   L   !     !     +-1dsz_B    
                                     !     !  
  --------KGVT--RG------------   L   !     !         +5cbz_E    
                                     !     !       +-7 
  --------KAVA--RA------------   L   +----15       ! ! +5e69_A    
                                           !       ! +-3 
  --------KGVT--RG------------   L         !     +-8   +2c7a_B    
                                           !     ! ! 
  --------KGVG------RA--------   L         !     ! ! +3g6t_A    
                                           !  +-11 +-5 
  --HAEC--KG--RGRG------------   L         !  !  !   +1a6y_A    
                                           !  !  !  
  ----ET--KGAT--RG------------   L         !  !  ! +1lat_A    
                                           +-14  +-6 
  --------KGVT--RG------------                !    +5emc_A    
                                              !  
  ----DG--KG--RTRG------------   L            !  +3cbb_A    
                                              +--4 
  --HC----KGVT--RG--RT--------                   +3g9m_B    
                                   


> 1m5x_B:CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-MSOI BOUND TO ITS DNA SUBSTRATE

  
  SAYCLCITRGDCYA----QG--------IGNARG----RG--DTIC--RG--   L                          +--2fld_B    
                                                                                    ! 
  SGIGQAKG----SC----KG------KGTA------YC--ST--VG--YA--   L            +-------------8    +6fb0_B    
                                                                      !             !  +-1 
  SGIGQAKGNC--SC----RGQG----DGTA--YC--AT--SC--VCKGRG--   L            !             +--2 +6fb0_A    
                                                                      !                ! 
  STITQAKGRG--STNT--QTST----ATTC------YT--SC--VCDTRGST   L            !                +3mxb_B    
                                                                      !  
  SANCSCKGLT----------DAEC--NATG--RCKGST------------DA   L   +-------12   +------------2ex5_A    
                                                             !        !   !  
  ST--NAVTHG--TCNA--ATLCYC--ECAT--YG--NA--SADCTCKTKGSA   L   !        !   !               +4lq0_A    
                                                             !        !   !             +-3 
  SGMGRGRG----KTYA--LTVT------TT----KT--SC--------RGEC   L   !        !   !           +-5 +4lox_A    
                                                             !        !   !           ! ! 
  STMG--------KGYC--RT--RG--VTSA----FC--MC----STQTRGEC   L   !        +--11           ! +5esp_A    
                                                             !            !         +-7 
  STIGRGRG------MC--LTEC----STKG----TT--NA------MGRTSC   L   !            !         ! ! +5t2n_A    
                                                           -13            !         ! +-6 
  SCMCRGRG----------YTST----ECTT--------RG----TTRG----   L   !            !  +------9   ! +5thg_A    
                                                             !            !  !      !   +-4 
  ------RARG------RTRGSTRT--QGTA--------SC----ATMCRGTC   L   !            !  !      !     +5t2h_A    
                                                             !            +-10      ! 
  CGRGST----------KARGQTFA--QGNG----HC--SC----LAQGRGQA   L   !               !      +--4yit_A    
                                                             !               !  
  YCST--------------YCTGET----EC------RG--RG------RGRG   L   !               +---------3uvf_B    
                                                             !  
  --YTLT------------------VT------QG--VG------RTEARGSC   L   +-------------------------2vs7_A    
                                                           


> 1mdy_C:CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION

  
  --------HGNT--LGEC----RCRC   L                     +-5i50_B    
                                                   +-3 
  KT----HGNT----EC----RCRG--   L                   ! +-1nkp_A    
                                                 +-5 
  ------HGNT--IAEC----YCRG--   L                 ! !  +1am9_A    
                                                 ! +--1 
  ------HGNT--MTEA----RCRG--   L              +--6    +1nlw_D    
                                              !  ! 
  --RT----NT--RGEC----RCQT--                  !  ! +---2ypa_A    
                                              !  +-4 
  ----HGNT--IAEC----RCRT----   L   +----------7    ! +-4ati_B    
                                   !          !    +-2 
  ------HGNT----EC----RCRG--   L   !          !      +-1nkp_E    
                                 --8          ! 
  ----HGST--ITET----RCRG----   L   !          +-------4h10_A    
                                   ! 
  --------HG----ITEC----RCRG   L   +------------------5nj8_D    
                                 


> 1mey_C:CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA

  
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L                         +1g2f_F    
                                                                 +-1 
  RG--DAQARG--RGSTDCHG--TTRG--DAEGRG--   L                +------2 +6b0o_A    
                                                          !      ! 
  QARGATNA----QA--ATHG----RG--DCNATT--   L              +-4      +2i13_A    
                                                        ! ! 
  ----TTSGRG------ECYC----NTYGQGFT----   L        +-----5 +-------5vmy_A    
                                                  !     ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L        !     !       +-5kl3_A    
                                                +-6     +-------3 
  EC--SCKGRG----TCYCKA--RGQA----TC----   L      ! !             +-5yeg_A    
                                             +--7 ! 
  ------------RG--DGEC--RGRGSGDCHA----   L   !  ! +---------------2wbs_A    
                                           --8  ! 
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L   !  +-----------------1tf6_A    
                                             ! 
  --TTTGECRG--RG----ET----RG--SCECRG--   L   +--------------------5v3j_F    
                                           


> 1mow_A:E-DREI

  
  --YTLT--YC----RGSGECRG----TG--QG--VG----DCTARTEARGSCSAIAQA--KG--NT--SCYA--QA----QA--TG--YC--RG--RG----VA----------------TC--   L                      +-------1mow_A    
                                                                                                                                                        !  
  ST------------AT--LCYC--EC--ATYG--NA--SADC--TCKTKGSACTFTST--YA--ST--KTST--ATQA--KT--TG--RA--RG--------AT--DT----TA----------   L                      !       +4lq0_A    
                                                                                                                                                     +-10     +-1 
  SGMGRG--------LT--VT------TT----KT--SC----------RGECSAKGIG--KT------SGIT--QAIA--QA--TC------DT--RG----WT--YC----TC----------   L                   !  !     ! +4lox_A    
                                                                                                                                                     !  !     ! 
  CGRG--ST--TTKARG--QTFA--QG--NG--HC--SC------LAQGRGQACCMT----AC--ST--AT----QAYA--IC--TA--RT------KGRT--VA--EC--QT------------   L                   !  +-----9   +4yit_A    
                                                                                                                                                     !        ! +-4 
  STMG----------RT----RGVT--SA--FC----MC------STQTRGECCTSTVA--FT--ST--TCSC--ATKA--IT--TC------STDA--RG--TC----KT--TG----------   L                   !        ! ! +5esp_A    
                                                                                                                                               +----12        +-8 
  STIGRG--------LT--EC--ST--KG----TT--NA--------MGRTSCHT--NC--WC--RG----------QG------ST--LA--KG--RG----WC----RG--TG----------   L             !     !          !   +5t2n_A    
                                                                                                                                               !     !          ! +-5 
  ------RA----------------------------SC------ATMCRGTCHC--NA--KT------------YA--RG----SA--RT--KG--KG----WT--ECET--TT----------   L             !     !          +-6 +5t2h_A    
                                                                                                                                            +-13     !            ! 
  SCMC--------------------------------RG------TTRG----TTYTHG----------------YCRGRGIT----------QC--------MC--HT----TGKT--------   L          !  !     !            +5thg_A    
                                                                                                                                            !  !     !  
  YCSTTC----KG--YC--TGET----EC------RG--RG--------RGRGCCST--YG--LTNT------YTITST----DT--AT----YA----TT--CC--RTKT--TA----------   L          !  !     +----------3uvf_B    
                                                                                                                                            !  !  
  ----------------------------------------------------SANCSC--KG--LT----------DAECNA--TG------RC------------------DA--QA----QC   L          !  +----------------2ex5_A    
                                                                                                                                     +-----14  
  ----------------------------------------------------SGIGQA--KG------SC----KG----KG--TA------YC--ST----VG----YA--------KCTG--   L   !      !                   +6fb0_B    
                                                                                                                                     !      !                 +-2 
  ----------------------------------------------------STITQA--KG--RG--STNT--QTST--AT--TC------YT--SC----VC--DTRG--ST----KGTG--   L   !      !               +-3 +3mxb_B    
                                                                                                                                     !      !               ! ! 
  ----------------------------------------------------SGIGQA--KG--NC--SC----RGQG--DG--TA--YC--AT--SC----VC--KGRG----------TT--   L -15      +---------------7 +6fb0_A    
                                                                                                                                     !                      ! 
  ----------------------------------------------------SAYCLC--IT--RGDCYA----QG--------IG----NA--RG--DT--IC----RG--------------   L   !                      +2fld_B    
                                                                                                                                     !  
  --YTLT--YC----RGSGECRGVT--TG--QG--VG------TARTEARGSC------------------------------WC--------DCDC--RGHA--VC------------------   L   !            +----------2vs7_A    
                                                                                                                                     +-----------11  
  YGRGRG----------------QG--EC------------------------------WADT----------------------------------NCKT------------------------   L                +----------3c0w_A    
                                                                                                                                   


> 1msw_D:STRUCTURAL BASIS FOR THE TRANSITION FROM INITIATION TO ELONGATION TRANSCRIPTION IN T7 RNA POLYMERASE

  
  RTKTNTQTKARAYTRGATYTDG--KG------RCRCYC--TC----TTYT--FARTQT--QGIGDG--------------HT--   L                  +-------------1msw_D    
                                                                                                 +----------3 
  --------------------------SC--EG----------QG--TGYGVGYT----QG------WGEGRG------------   L     +-4          +-------------4boc_A    
                                                                                               ! ! 
  --------------------------------RC--YC----------------------------------------------       +-5 +------------------------6dta_A    
                                                                                             ! ! 
  ----------------------------------------------TCYC----------------------------------     --6 +--------------------------6dta_B    
                                                                                             ! 
  ----------------------------KT----RG--EG----YGACYCAC--------------------RTNG--QG--HC   L   !                    +------4xvk_A    
                                                                                             +--------------------2 
  ----------------------------KC--------------FG--YGMG----------------------NG--QG--HG   L                        ! +----4bwj_A    
                                                                                                                  +-1 
  ----------------------NA--KA------RG------QC----YCMC------------------------QC------                              +----4x0q_B    
                                                                                           


> 1nfk_A:STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER

  
  RGRGYTCCEC----HTKTKTPTKTRG   L                +--1nfk_A    
                                              +-3 
  RGRGYTCCEC----HG--KG------   L   +----------4 +--1a3q_A    
                                   !          ! 
  RGRGYTCTEC--------RT------   L   !          +---1gji_A    
                                 --5 
  RGRG----EC--------RGPTKT--   L   !                +2ram_A    
                                   !              +-1 
  RGRGYTCTEC--SG----RT------   L   +--------------2 +2i9t_A    
                                                  ! 
  RGRGYTCTECRG------KT------   L                  +3do7_A    
                                 


> 1nk3_P:VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE



> 1nkp_A:CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA

  
  KT--HGNT----ECRCRG   L                                +1nkp_A    
                                                     +--1 
  ----HGNT--LGECRCRC   L                           +-7  +5i50_B    
                                                   ! ! 
  ----HGNT----ECRCRG   L               +----------10 +--1nkp_E    
                                       !           !  
  ----HGNT--IAECYCRG   L               !           !   +1am9_A    
                                       !           +---4 
  ----HGNT--MTEARCRG   L               !               +1nlw_D    
                                       !  
  ----HGNT--LCECRCRG   L               !                +1hlo_B    
                               +------14             +--5 
  ----HGNT--IAECRCRT   L       !       !     +-------9  +4ati_B    
                               !       !     !       ! 
  --RT--NT--RGECRCQT           !       !     !       +---2ypa_A    
                               !       !  +-11  
  --RG--TT--RAECRC--           !       !  !  !        +--1mdy_C    
                               !       !  !  +--------8 
  ----HGST--ITETRCRG   L       !       +-12           !  +4h10_A    
                           +--15          !           +--3 
  ----HG----ITECRCRG   L   !   !          !              +5nj8_D    
                           !   !          !  
  ----HG------ETRTRG   L   !   !          +--------------5v0l_A    
                           !   !  
  ----RTNT----ECRCRG   L   !   !                       +4h10_B    
                         -16   !       +---------------2 
  ----ST------ATRTRG       !   !       !               +4zpk_B    
                           !   +------13  
  ------NT----ETRCMT       !           !             +-2ql2_D    
                           !           +-------------6 
  --------NG--SCHTRC       !                         +-5nj8_C    
                           !  
  ----HG------ETRCRG   L   +---------------------------5gnj_I    
                         


> 1nkp_E:CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA

  
  HGNTLGEC--RCRC------   L                    +--5i50_B    
                                            +-3 
  HGNT--EC--RCRG------   L                  ! ! +1nkp_E    
                                            ! +-2 
  HGNT--EC--RCRG------   L                  !   +1nkp_A    
                                         +--6 
  HGNTMTEA--RCRG------   L               !  !     +1nlw_D    
                                         !  ! +---1 
  --------HG----ECYCRG   L               !  +-5   +1am9_A    
                             +-----------7    ! 
  HGNTIAEC--RCRT------   L   !           !    +---4ati_B    
                             !           ! 
  --NTRGEC--RCQT------     --8           !    +--2ypa_A    
                             !           +----4 
  HGSTITET--RCRG------   L   !                +--4h10_A    
                             ! 
  HGKT--EA--RCRC------   L   +-------------------1a0a_B    
                           


> 1nlw_D:CRYSTAL STRUCTURE OF MAD-MAX RECOGNIZING DNA

  
  ----HGNT----EC----RCRG------   L                           +1nkp_A    
                                                           +-1 
  ----HGNT--LGEC----RCRC------   L                         ! +5i50_B    
                                                         +-3 
  --------HGNT--IAEC----YCRG--   L                       ! ! +1am9_A    
                                                +--------6 +-2 
  ----HGNT--MTEA----RCRG------   L              !        !   +1nlw_D    
                                                !        ! 
  ----HGNT----EC----RCRG------   L              !        +---1nkp_E    
                                          +-----8 
  ----HGNT--IAEC----RCRT------   L        !     !        +---4ati_B    
                                          !     !      +-5 
  RT----NT--RGEC----RCQT------            !     !      ! +---2ypa_A    
                                     +----9     +------7 
  ----HGST--ITET----RCRG------   L   !    !            !  +--4h10_A    
                                     !    !            +--4 
  --QG------VTEC----RCRG----QG   L -10    !               +--1an4_A    
                                     !    ! 
  RG--HGKT----EA----RCRC------   L   !    +------------------1a0a_B    
                                     !  
  --------NG--SC----HTRC------       +-----------------------5nj8_C    
                                   


> 1nwq_C:CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX

  
  --------RG------NC--YGAT--CTRG   L     +------2wt7_B    
                                         ! 
  ----RC----NC----AAAT--CTRC----   L     !         +2wt7_A    
                                       +-5       +-2 
  ----------------NTRTATAT--CTRA   L   ! !     +-3 +5vpe_D    
                                       ! !     ! ! 
  RG----NC----YGAT----RC--------   L   ! +-----4 +4eot_A    
                                     --6       ! 
  ----------RA----NA--AAVT--STRG   L   !       ! +1nwq_C    
                                       !       +-1 
  --RG--QGNART--AGQT--FTRG------   L   !         +1gd2_G    
                                       ! 
  ----------------NCTT--AT----RG   L   +--------2dgc_A    
                                     


> 1oe4_B:XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE

  
  VGRG------PG--------NG          +--------------1oe4_B    
                               +--3 
  ------RANT--QGTC--RC--   L   !  +--------------2dp6_A    
                             --4 
  --------------PTLT----       !              +--5nnu_A    
                               !            +-1 
  ----------PALA--------       +------------2 +--4uqm_A    
                                            ! 
  KT--TT----------------                    +----4yig_E    
                             


> 1orn_A:STRUCTURE OF A TRAPPED ENDONUCLEASE III-DNA COVALENT INTERMEDIATE: ESTRANGED-GUANINE COMPLEX

  
  ----QGCGTA----LC------------------------                                +-1orn_A    
                                                                   +------6 
  ----------------YG--------------------RG   L                     !      +-5kn8_A    
                                                                   ! 
  ----NCNANARC--------YGRC----------------                 +-------9     +---2xhi_A    
                                                           !       ! +---7 
  ----NG--RG--------FGRC------------------                 !       ! !   !   +4ejy_A    
                                                           !       ! !   +---1 
  ----NA--RA--------FGRC------------------   L             !       +-8       +3i0w_A    
                                                           !         ! 
  ----QTLAHGAT--------KT------------------           +----10         !      +3s6i_A    
                                                     !     !         +------4 
  --QGKGLGSGAG--SC--LTKC------------------           !     !                +4b21_A    
                                                     !     !  
  --NGRGTG------LG----LCRG----------------           !     !                 +4ew0_A    
                                                 +--11     !               +-2 
  LTNGRGTG------LC----LCRG--------YTNTKT--       !   !     +---------------3 +4ofa_A    
                                                 !   !                     ! 
  --NGRGTG------LG----LCRG----------------       !   !                     +4e9f_A    
                                               -12   !  
  --AA--LA----ITHT----KT------------------       !   +----------------------2ofi_A    
                                                 !  
  ------------------------IAQCNAYA--------   L   !                         +1nk3_P    
                                                 +-------------------------5 
  ------------------------VASGNA----------   L                             +3cmy_A    
                                               


> 1p7h_L:STRUCTURE OF NFAT1 BOUND AS A DIMER TO THE HIV-1 LTR KB ELEMENT

  
  RG--YTTTECRGRCQA------KARC   L              +-------------------1p7h_L    
                                              ! 
  RGRGYTEC------RT----------   L     +--------3                  +-1gji_A    
                                     !        !                +-1 
  ----------------PT--RG----   L     !        +----------------2 +-1nfk_A    
                                   +-4                         ! 
  RGRGYTEC--HG--KG----------   L   ! !                         +--1a3q_A    
                                 --5 ! 
  ------------------FG------   L   ! +----------------------------6f59_B    
                                   ! 
  ----------------------RT--       +----------------------------4oi8_B    
                                 


> 1pp7_U:CRYSTAL STRUCTURE OF THE T. VAGINALIS INITIATOR BINDING PROTEIN BOUND TO THE FERREDOXIN INR

  
  KTHG----------------------                            +5hdn_C    
                                           +------------1 
  ----------ST--RTQTMT------   L   +-------3            +5d8k_B    
                                   !       ! 
  ----------KT--RGYA--------   L --4       +-------------1bc8_C    
                                   ! 
  --------KATG--LTRT--KAFTYT   L   !                +----2p7c_B    
                                   +----------------2 
  ----STPTATATTT------------   L                    +----5yi2_J    
                                 


> 1pue_E:PU.1 ETS DOMAIN-DNA COMPLEX

  
  ----DCKTRG----RGYA------   L                        +1dux_F    
                                                    +-1 
  ------KTRGAT--RGYA------   L                    +-4 +1bc8_C    
                                                  ! ! 
  ------KTRGSA--RGQA----RA   L          +---------5 +1yo5_C    
                                        !         ! 
  ------KTRGAT--RGYT------   L   +------7         +-1awc_A    
                                 !      ! 
  KTHG--------------------       !      !          +5hdn_C    
                                 !      +----------2 
  ------ST------RTQT--MT--   L --8                 +5d8k_B    
                                 ! 
  ----KG--ATNT--CT----SC--   L   !                  +2irf_L    
                                 !                +-3 
  --------NT--RGCT--NGST--   L   +----------------6 +1if1_B    
                                                  ! 
  --------------------RG--                        +-4hly_B    
                               


> 1puf_A:CRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA



> 1puf_B:CRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA



> 1qbj_C:CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX

  
  ------------------ST------STQAQGST--SART--------------------KT--------   L   +------------------------5trd_B    
                                                                               !  
  --------------------RG----STRGMCTT--RT--------------------------------   L   !                              +4u0y_B    
                                                                               !                           +--8 
  --------------------------TTLTECTA--STRG------------------------------   L   !        +-----------------12  +4i2o_B    
                                                                               !        !                  !  
  --------------------------ITRGECSC--SGKG------------------------------   L   !        !                  +---5i2d_R    
                                                                               !        !  
  --------------------------TT--PTTC--STNT--------------------RT--------   L   !        !                         +4lln_I    
                                                                               !        !                       +-7 
  --------------------------LTRTPTNA--VT----------------------RT--------   L   !        !                   +---9 +6c2s_D    
                                                                               !        !                   !   ! 
  --------------------------DCSA--TA--TT--------RT------------RA--------   L   !        !          +-------13   +1z9c_A    
                                                                               !        !          !        !  
  ----------------------------RGSTRT--STHG--------------------RA--------   L   !        !          !        +----3zpl_B    
                                                                               !        !          !  
  --------------------------STKTPTTT--FT----------------------RA--------   L   !        !     +---22        +-----4aso_F    
                                                                               !        !     !    !     +-14  
  --------------------------STQASGAT--STQT--------------------QA--------   L   !        !     !    !     !  +-----4on0_B    
                                                                               !        !     !    +----16  
  --------------------------------------------YG------------------------       !        !     !          !       +4lb5_B    
                                                                               !     +-26     !          !   +---5 
  ------------------TT----------KATT--QTTG----LTRT----KA----------FT--YT   L   !     !  !     !          +--11   +2p7c_B    
                                                                               !     !  !     !              !  
  --------------------------TT--RGRT--------------------------KT--------   L -29     !  !     !              +---2v1u_A    
                                                                               !     !  !     !  
  --------------------SGQG----YCNC--------------------------------------       !     !  !     !                     +2ve9_C    
                                                                               !     !  !  +-24                   +-1 
  --------LAHAKARA--------------------------------------------------IAVA       !     !  !  !  !        +----------6 +6dta_A    
                                                                               !     !  !  !  !        !          ! 
  --------------------------------------------YGRG----------------------       !     !  !  !  !     +-20          +4wcg_B    
                                                                               !     !  !  !  !     !  !  
  --------------------------QTPTPG--TTRG----------------------HT--------   L   !     !  !  !  !     !  +-----------5xxp_A    
                                                                               !     !  !  !  !  +-21  
  ------------------------------RGRG--YC--------------------------------   L   !     !  !  !  !  !  !             +1cf7_A    
                                                                               !     !  !  !  !  !  !    +--------3 
  ----TTQT--------------------------------------------------------------   L   !     !  !  !  !  !  !    !        +3gpl_A    
                                                                               !     !  !  !  !  !  +---17  
  --------------------------------------------YG------------------------       !  +-27  +-25  !  !       !        +2heo_D    
                                                                               !  !  !     !  +-23       +--------4 
  ------------------------------KGTA----TA------RG----------------------   L   !  !  !     !     !                +1xsd_A    
                                                                               !  !  !     !     !  
  --------------------------------------------YG------------------------       !  !  !     !     !                 +4ka4_B    
                                                                               !  !  !     !     !               +-2 
  ------------------------------HT----RTITYT----------------------------   L   !  !  !     !     !     +--------10 +4kfc_B    
                                                                               !  !  !     !     !     !         !  
  ----------------------------RG----DTVT----ST------------RC------------   L   !  !  !     !     +----19         +4nhj_A    
                                                                               !  !  !     !           !  
  ------------------------------NTVC--ECSTYT--STYC--------RA------------   L   +-28  !     !           +----------5ed4_A    
                                                                                  !  !     !  
  MTPT--------------------RT--------------------------------------------   L      !  !     +--------------------5fmf_V    
                                                                                  !  !  
  --------------------------------------NA----HT--STLT------------------   L      !  !                 +-----2a07_K    
                                                                                  !  !            +---15  
  ------------------------------------NAST--RTHT--ST--------------------   L      !  +-----------18    +-----3l2c_A    
                                                                                  !               !  
  --------------KAFA------------------------------------YANAKTFGMC------          !               +----------3aaf_B    
                                                                                  !  
  --------------------------------------------------------------ITHG----   L      +-----------------------5iyc_T    
                                                                             


> 1qna_B:CRYSTAL STRUCTURE OF THE T(-30) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.

  
  NTVTFT--LTFAVATTNAVTFTPALTFAVATA   L                  +1qna_B    
                                               +--------3 
  NTVAFT--LTFAVATTNAVTFAPALAFTVATA   L         !        ! +1cdw_A    
                                             +-4        +-1 
  NTVAFC--LTFAVATTNAVTFTPALTFTVATA   L       ! !          +4wzs_D    
                                             ! ! 
  NTVAFT--LTFAVATTNAVAFAPALTFTVATA   L   +---5 +---------1rm1_A    
                                         !   ! 
  NTVTFA--LAFTVATTNAVTFTPALTFAVTTA   L   !   !          +5n9g_G    
                                       --6   +----------2 
  NAVTFTPALTFAVATANTVTFTPALTFAVAST   L   !              +1ais_A    
                                         ! 
  NAVTFT--LTFAVATANTVTFAPALAFTVATA   L   +--------------1ytb_A    
                                       


> 1qpi_A:CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX

  
  --RC----PTTC--WC   L     +---------------1qpi_A    
                         +-8 
  TTHTRTQAATSCYTYT   L   ! !     +---------5dy0_D    
                         ! +-----6 
  ----TGKG----YCFA   L   !       +---------4pxi_B    
                       --9 
  ----SCKGSG--IGYC   L   !   +-------------2yvh_A    
                         !   ! 
  --EC--KGQCTGYGRC   L   !   !          +--4jl3_B    
                         +---7       +--3 
  TA--AT----LCFGHA           !   +---4  +--4i6z_B    
                             !   !   ! 
  --PTTCRG----YGHA   L       !   !   +-----6c31_A    
                             +---5 
  TA----ECAC--YCRA               !          +5haw_A    
                                 !        +-1 
  TA--STECAGATYTRG   L           +--------2 +4gck_A    
                                          ! 
  VT--AGDT--TTYTLA   L                    +5gpc_B    
                       


> 1qpz_A:PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

  
  ----SG--TC------RG------LCKA   L             +1qpz_A    
                                     +---------2 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   !         ! +3oqm_C    
                                   --3         +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L   !           +1rzr_C    
                                     ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   +----------1efa_B    
                                   


> 1qrv_A:CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA

  
  ----STYGLASGLA--TGTCIT--   L   +-----------------3tq6_B    
                                 ! 
  RTTASTYAFALT----PTATSTRA   L --4 +---------------5jh0_D    
                                 ! ! 
  RT--NTFTMA--RT--NG--SA--   L   +-3              +4y60_C    
                                   !            +-1 
  KC--NT--MAMA--EGSAACNT--   L     +------------2 +2lef_A    
                                                ! 
  RC--NTFTMA--RAHGNT--SA--   L                  +--3f27_D    
                               


> 1qzh_E:CRYSTAL STRUCTURE OF POT1 (PROTECTION OF TELOMERE)- SSDNA COMPLEX

  
  --NG--------------STTT--DT--------QC--HC--FA--------TGRGYCRCQC--LGSGKGDG             +----------------------6bwy_A    
                                                                                     +-2 
  ----------------------------YTFT----NT--SG--WG--------KGFG--EGKG--KG----           ! +----------------------3u58_C    
                                                                                 +---3 
  ------KGFG--------ST--TTDT------TGTG--LA--FA----------QGYG--QG--IA------   L   !   !    +------------------3kjp_A    
                                                                               --4   +----1 
  --------DGTGFGYGKT--------YT----KG------------FGIGHG--RGYG--QG----------   L   !        +------------------2i0q_A    
                                                                                 ! 
  EGTGYG------------------------------KG--------------KT--YG--------------   L   +---------------------------1s40_A    
                                                                               


> 1r4i_A:CRYSTAL STRUCTURE OF ANDROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO A DIRECT REPEAT RESPONSE ELEMENT

  
  ----EA--KG--RTRTRT              +--2han_B    
                              +--13  
  ----EC--KG--KGRG--   L      !   !  +-1dsz_B    
                              !   +-11  
  --------KGVT--RG--   L      !      ! +5cbz_E    
                              !      +-1 
  ----EC--KA--RGRG--   L      !        +4nqa_I    
                           +-16  
  --HGECAGKGAAKGRT--   L   !  !    +-1lo1_A    
                           !  !  +-9 
  ----EC--KG--KGRA--   L   !  !  ! ! +5l0m_A    
                           !  !  ! +-3 
  ----EC--KG--KGRG--   L   !  +-15   +2ff0_A    
                           !     !  
  --------KGVT--RG--   L   !     !  +2c7a_B    
                           !     +--7 
  --------KAVA--RA--   L   !        ! +5e69_A    
                           !        +-2 
  ----EC--KG--RGRG--   L -17          +2nll_B    
                           !  
  --------VG--RG----   L   !           +3g6t_A    
                           !         +-6 
  --HC----KGVT--RG--       !      +-10 +3g9m_B    
                           !      !  !  
  --HAEC--KG--RGRG--   L   !      !  +-1a6y_A    
                           !   +-12  
  ----DG--KG--RTRG--   L   !   !  !   +3cbb_A    
                           !   !  ! +-4 
  CA--EC--KG--KGRG--   L   !   !  ! ! +1cit_A    
                           +--14  +-8 
  ----ET--KGAT--RG--   L       !    ! +1lat_A    
                               !    +-5 
  ----EA--KG--RTRG--   L       !      +1kb2_B    
                               !  
  --------KGVT--RG--           +---5emc_A    
                         


> 1r71_C:CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF KORB IN COMPLEX WITH THE OPERATOR DNA

  
  --STPTAAFTTTQC--DGTC--RG----   L                   +----1r71_C    
                                     +---------------2 
  ETSGRGAT--ATNTRT----KCVTRTEC   L   !               +----4umk_D    
                                   --3 
  --SGRAAT--TTRG--------------   L   !                    +3vwb_A    
                                     +--------------------1 
  --SGQAAT--TTRG--------------   L                        +1zx4_A    
                                   


> 1r8d_B:CRYSTAL STRUCTURE OF MTAN BOUND TO DNA

  
  --RGHTHCYG   L                       +1r8d_B    
                       +---------------3 
  --KCRT--YC           !               +1r8e_A    
                       ! 
  --KGRT----   L   +---5                 +5i44_I    
                   !   !               +-1 
  --RART----       !   !          +----2 +4r24_B    
                   !   !          !    ! 
  --RGRTYTRT   L --6   +----------4    +4r4e_B    
                   !              ! 
  --KGRTFCYG   L   !              +-----4wls_B    
                   ! 
  DCKG--RAHT   L   +--------------------6ama_L    
                 


> 1r8e_A:CRYSTAL STRUCTURE OF BMRR BOUND TO DNA AT 2.4A RESOLUTION

  
  KCRT--YC--               +--------------------1r8e_A    
                           ! 
  RGHTHCYG--   L   +-------5        +-----------1r8d_B    
                   !       !        ! 
  KGQGRT----   L   !       !        !            +5i44_I    
                   !       +--------4          +-1 
  RART------       !                !      +---2 +4r24_B    
                 --6                !      !   ! 
  RGRTYTRT--   L   !                +------3   +4r4e_B    
                   !                       ! 
  KGRTFCYG--   L   !                       +----4wls_B    
                   ! 
  --------RG   L   +----------------------------1nlw_D    
                 


> 1rep_C:CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA

  
  ------SGAAECSAKGRGRG--STYGRTPGDCRGRG--RC   L                          +--1rep_C    
                                                 +----------------------1 
  ----TT--SGLTYART--------YT--PCITRGDCKT--   L   !                      +--2nra_C    
                                               --4 
  ----TT--PTTCSTNT----RT------------------   L   !        +----------------4lln_I    
                                                 ! +------2 
  --------RGRGYC--------------------------   L   +-3      +----------------1cf7_A    
                                                   ! 
  LTETTTRAECRCRCQC------------------------   L     +-----------------------3n97_A    
                                               


> 1rio_A:STRUCTURE OF BACTERIOPHAGE LAMBDA CI-NTD IN COMPLEX WITH SIGMA-REGION4 OF THERMUS AQUATICUS BOUND TO DNA

  
  KGKG------QASG----------NG   L                +-1rio_A    
                                      +---------2 
  KGKG--ET--QASG----------NG   L      !         +-1lmb_4    
                                   +--4 
  ----QT--STNTVTATSTQTRTETTT   L   !  !          +2r1j_L    
                                   !  !      +---1 
  ----------SCATRTNCQT----HT   L --5  +------3   +4jcy_A    
                                   !         ! 
  ------AT--QAAT--SA--------       !         +----4z5h_A    
                                   ! 
  --------TT----ATYTQTQT----   L   +--------------3qws_B    
                                 


> 1rio_H:STRUCTURE OF BACTERIOPHAGE LAMBDA CI-NTD IN COMPLEX WITH SIGMA-REGION4 OF THERMUS AQUATICUS BOUND TO DNA

  
  --LTEGTT--ETRC--RC----------   L                             +-------------6b6h_F    
                                                     +---------5 
  ------TTRTECRC--RCQC--------   L              +----8         +-------------6c04_F    
                                                !    ! 
  --YG--------TG--RGSG--FTRG--   L              !    +-----------------------2h27_A    
                                                ! 
  --LTETTTRAECRC--RCQC--------   L              !                          +--3n97_A    
                                              +-9                        +-1 
  ------TT--PTTC--STNT--------   L            ! !            +-----------3 +--4lln_I    
                                              ! !            !           ! 
  --------RGSTRT--STHG--------   L            ! !      +-----6           +---3zpl_B    
                                              ! !      !     ! 
  ------STKTPTTT--FT----------   L            ! !      !     +---------------4aso_F    
                                           +-10 +------7 
  --TT------KATT--QTTG--LTRTKA   L         !  !        !                 +---2p7c_B    
                                           !  !        !               +-2 
  ------TT--RG----ST----------   L         !  !        +---------------4 +---2qby_A    
                                        +-11  !                        ! 
  ------ST--RG----------------   L      !  !  !                        +-----2qby_B    
                                        !  !  !  
  ------TT--SGLT--YART--------   L   +-12  !  +-----------------------------2nra_C    
                                     !  !  !  
  QT--------------------------       !  !  +-----------------------------6f40_V    
                                   -13  !  
  --------RG----DTVT--STRG----   L   !  +-----------------------------4nhj_A    
                                     !  
  --------------RGAC--LG------       +-----------------------------4wx9_A    
                                   


> 1rpe_R:THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION

  
  QT--STNTVTATSTQTRTETTT   L                        +-2r1j_L    
                                              +-----2 
  ------SCATRTNCQT----HT   L                +-3     +-4jcy_A    
                                            ! ! 
  --AT--QAAT--SA--------               +----4 +-------4z5h_A    
                                       !    ! 
  --ET--QASG----------NG   L           !    !         +1lmb_4    
                               +-------5    +---------1 
  ------QASG----------NG   L   !       !              +1rio_A    
                             --6       ! 
  ----TT----ATYTQTQT----   L   !       +--------------3qws_B    
                               ! 
  ----TTQA--LTSAET------   L   +----------------------2o4a_A    
                             


> 1rxw_A:CRYSTAL STRUCTURE OF A. FULGIDUS FEN-1 BOUND TO DNA

  
  ----------ICIC--QG--TGLGKGSG----------------------RC                       +-1rxw_A    
                                                             +---------------1 
  --------IA--AGVG--QC--LCQCMG------------KCKA------RC       !               +-5k97_A    
                                                           --4 
  CTHTKA------------------------RT------RC----RG------       !    +------------5v07_Z    
                                                             ! +--2 
  ITYTQT--KTAA----------------------------------------       +-3  +------------4q0w_A    
                                                               ! 
  ------FCRT------------------LT--TGEGEG--------FTRT--   L     +---------------5hp4_A    
                                                           


> 1rzr_C:CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR- PHOSPHOPROTEIN-DNA COMPLEX

  
  IT--ST--ATTTSTRG----VTAGLCAC   L               +1rzr_C    
                                               +-1 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   +---------2 +3oqm_C    
                                     !         ! 
  ----SG--TC------RG------LCKA   L --3         +1qpz_A    
                                     ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   +---------1efa_B    
                                   


> 1s40_A:SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER

  
  EGTGYG--SG--DGKGATFTSGVGNGYTLGYGYGKG--YT--RGDGNG--KT--YG--NGAG--RT--   L              +---------------1s40_A    
                                                                                     +--1 
  ----YT--------------------------------YGDG----------------------RT--   L           !  +---------------3kjp_A    
                                                                             +-------3 
  ----QT------------------------------RT----------LTTTKTFTQT----ST--HT       !       !  +---------------4gnx_B    
                                                                           --4       +--2 
  ------KG--WGYT--------YCFA--MA--RGRTIGWGDG--------------------------   L   !          +---------------4hja_A    
                                                                             ! 
  --KG--------------------------------MTFT----------------------------   L   +--------------------------6d6v_D    
                                                                           


> 1sax_A:THREE-DIMENSIONAL STRUCTURE OF S.AUREUS METHICILLIN-RESISTANCE REGULATING TRANSCRIPTIONAL REPRESSOR MECI IN COMPLEX WITH 25-BP DS- DNA

  
  ----------------------KGTA--TA----RG----------------   L                    +-----------1xsd_A    
                                                                              !  
  ----------TT----------KATTQTTG--LTRT----KA----FT--YT   L                +--14      +----2p7c_B    
                                                                          !   !    +-6 
  --------------------SANCTGTTPT----------------RT----   L                !   +---10 +----5hlg_E    
                                                                          !        !  
  ------------------LTRTPTNAVT------------------RT----   L            +--15        +------6c2s_D    
                                                                      !   !  
  --------------------------------YG------------------                !   !              +4lb5_B    
                                                                      !   !       +------2 
  ------------------DCSA--TATT------RT----------RA----   L            !   +------11      +1z9c_A    
                                                                      !           !  
  ----------ST------STQAQGSTSART------------KT--------   L            !           +-------5trd_B    
                                                                   +-16  
  ------------SG--QG--YCNC----------------------------             !  !                   +2ve9_C    
                                                                   !  !       +-----------1 
  LAHAKARA----------------------------------------IAVA             !  !       !           +6dta_A    
                                                                   !  !       !  
  --------------------------------YG------------------             !  !       !               +4ka4_B    
                                                                   !  !       !             +-3 
  --------------------------------YGRG----------------             !  +------13           +-4 +4wcg_B    
                                                                   !          !           ! ! 
  ----------------------RGRGYC------------------------   L      +-17          !       +---5 +1cf7_A    
                                                                !  !          !       !   ! 
  ------------------ST--PTTC--QG----RG----------------   L      !  !          !     +-7   +1f5t_A    
                                                                !  !          !     ! ! 
  --------------------------------YG------------------          !  !          +-----8 +----2heo_D    
                                                                !  !                ! 
  --------------RG--STRGMCTTRT------------------------   L      !  !                +-----4u0y_B    
                                                             +-18  !  
  ----------------------------NA--HT--STLT------------   L   !  !  !              +-----2a07_K    
                                                             !  !  !           +--9 
  --------------------------NASTRTHT--ST--------------   L   !  !  +----------12  +-----3l2c_A    
                                                           -19  !              !  
  ------KAFA--------------------------------------MC--       !  !              +--------3aaf_B    
                                                             !  !  
  ------------YC----KTHGSTQTYTPT--------------LG------   L   !  +-----------------------5x11_A    
                                                             !  
  ----------------------DCKT--RG--RGYA----------------   L   +-------------------------1dux_F    
                                                           


> 1sfu_A:CRYSTAL STRUCTURE OF THE VIRAL ZALPHA DOMAIN BOUND TO LEFT- HANDED Z-DNA

  
  ------------ST------STQAQGST--SART--------------KT--------   L               +-----------------------5trd_B    
                                                                               !  
  ------------------------RGRG--YC--------------------------   L               !                         +--1cf7_A    
                                                                               !                +--------8 
  ------------------------------------YG--------------------                   !                !        !  +2heo_D    
                                                                               !                !        +--3 
  --------------------ST--PTTC----QG----RG------------------   L               !                !           +1f5t_A    
                                                                               !             +-16  
  ------------------------------------YGRG------------------                   !             !  !           +4wcg_B    
                                                                               !             !  !  +--------2 
  ----LAKARA--------------------------------------------IAVA                   !             !  +-13        +6dta_A    
                                                                               !             !     !  
  ------------------------KGTA----TA----RG------------------   L               !             !     +--------1xsd_A    
                                                                               !             !  
  ------------------------------------YG--------------------                   !             !               +4lb5_B    
                                                                               !        +---18             +-1 
  --------------------TT--PTTC--STNT--------------RT--------   L               !        !    !         +---6 +4lln_I    
                                                                               !        !    !         !   ! 
  ----------------------RGSTRT--STHG--------------RA--------   L            +-24        !    !     +--11   +-3zpl_B    
                                                                            !  !        !    !     !   !  
  --------------------STPTATAT--TTKG------------------------   L            !  !        !    !  +-14   +-----5yi2_J    
                                                                            !  !        !    !  !  !  
  --------------------STKTPTTT--FT----------------RA--------   L            !  !        !    !  !  +---------4aso_F    
                                                                            !  !     +-20    +-17  
  ------------------------------------YG--------------------                !  !     !  !       !           +4ka4_B    
                                                                            !  !     !  !       !        +--4 
  ------------TT----------KATT--QTTG--LTRT----KA------FT--YT   L            !  !     !  !       !        !  +2p7c_B    
                                                                            !  !     !  !       +--------9 
  --------------SGQG----YCNC--------------------------------                !  !     !  !                ! +--2ve9_C    
                                                                            !  !     !  !                +-7 
  --------------------QTPTPG--TTRG----------------HT--------   L            !  !  +-21  !                  +--5xxp_A    
                                                                            !  !  !  !  !  
  ITPT--------------RT--------------------------------------   L            !  !  !  !  +-------------------5fmf_V    
                                                                         +-25  !  !  !  
  --------------------------------NA--HT--STLT--------------   L         !  !  !  !  !              +-----2a07_K    
                                                                         !  !  !  !  !         +---12  
  ------------------------------NASTRTHT--ST----------------   L         !  !  +-22  !    +---15    +-----3l2c_A    
                                                                         !  !     !  !    !    !  
  --------KAFA------------------------------------FG--------             !  !     !  +---19    +----------3aaf_B    
                                                                         !  !     !       !  
  --------------YC----KTHGSTQT--YTPT------------------------   L         !  !     !       +---------------5x11_A    
                                                                         !  !     !  
  --------------------------------------------------HG------   L      +-26  !     +----------------------5iyc_T    
                                                                      !  !  !  
  --------------RG----STRGMCTT--RT--------------------------   L      !  !  !                        +4u0y_B    
                                                                      !  !  !                     +--5 
  --------------------TTLTECTA--STRG------------------------   L      !  !  !  +-----------------10  +4i2o_B    
                                                                      !  !  !  !                  !  
  --------------------ITRGECSC--SGKG------------------------   L   +-27  !  +-23                  +---5i2d_R    
                                                                   !  !  !     !  
  ----------------------RG----DTVT--STRG--------RC----------   L   !  !  !     +----------------------4nhj_A    
                                                                   !  !  !  
  --KC------------------MGSGTT--TTYC------------------------   L -28  !  +--------------------------5f7q_C    
                                                                   !  !  
  --------------------------AA----ET--------------RG--------   L   !  +----------------------------5eix_A    
                                                                   !  
  ------------------------FT--------------------------------   L   +-----------------------------1u8b_A    
                                                                 


> 1t2k_D:STRUCTURE OF THE DNA BINDING DOMAINS OF IRF3, ATF-2 AND JUN BOUND TO DNA

  
  --------------NTRTATAT--CTRA------   L                        +5vpe_D    
                                                              +-1 
  --RG----NC----YGAT----RC----------   L                      ! +4eot_A    
                                                    +---------5 
  RG--QGNART--AGQT--FTRG------------   L            !         !   +1gd2_G    
                                                    !         ! +-2 
  ----------------RG----NC--YGATCTRG   L            !         +-4 +2wt7_B    
                                             +------7           ! 
  --RC----NC----AAAT--CTRC----------   L     !      !           +2wt7_A    
                                             !      ! 
  --------NCRT--ATAT--STRG----------   L     !      !          +1t2k_D    
                                           +-8      +----------3 
  --------RA----NA--AAVT--STRG------   L   ! !                 +1nwq_C    
                                           ! ! 
  ----------------NT--ATAT--STRG----   L --9 !             +---1dh3_C    
                                           ! +-------------6 
  --------NCTT----AT----RG----------   L   !               +---2dgc_A    
                                           ! 
  --RG----NT----ATAT----RG----------   L   +-----------------5vpe_C    
                                         


> 1t38_A:HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE

  
  RGAC--                               +--1t38_A    
               +-----------------------2 
  RAAC--       !                       !  +1yfh_A    
             --3                       +--1 
  RGACLG       !                          +4wx9_A    
               ! 
  ----YG       +--------------------------2heo_D    
             


> 1t9i_B:I-CREI(D20N)/DNA COMPLEX

  
  STITQANG------ST--------RG--RG--YCTCYC--RG------VCQT------KGTC--   L                                 +3mxb_R    
                                                                                                     +-1 
  SGIGQAKG------SC--------KG------KGTA----YC--ST--VG--YA----KCTG--   L                             +-2 +6fb0_B    
                                                                                                   ! ! 
  STITQAKG--RG--STNT------QT--ST--ATTC----YT--SC--VCDTRGST--KGTG--   L                           +-3 +3mxb_B    
                                                                                                 ! ! 
  SGIGQAKG--NC--SC--------RG--QG--DGTAYC--AT--SC--VCKGRG------TT--   L                  +--------8 +6fb0_A    
                                                                                        !        ! 
  SAYCLCIT--RGDCYA--------QG--------IG--NA--RG--DTIC--RG----------   L              +--13        +2fld_B    
                                                                                    !   !  
  STITQAKG--RG--STNT------QG--ST--ATTC----YT--SC--VCDTRGST--KGTG--   L              !   !       +2xe0_B    
                                                                                    !   +------10  
  SANCSCKG--LT----------------DAECNATG----RC------------DAQA----QC   L              !           +2ex5_A    
                                                                                    !  
  SAYCKTIT--RGDCYA------------------IG------RG--DTIC----IA--------   L              !     +-------1m5x_B    
                                                                                    !     !  
  ST--NAVT--HG--TCNA------AT--LCYCECAT----YG--NA--TCKTKGSA--------   L   +---------15     !           +4lq0_A    
                                                                         !          !     !         +-4 
  SGMGRGRG------KTYA------LT--VT----TT----KTSC--------RGEC--------   L   !          !     !       +-7 +4lox_A    
                                                                         !          !  +-12       ! ! 
  STMG----------KGYC------RT----RGVTSA----FCMC----STQTRGEC--------   L   !          !  !  !       ! +5esp_A    
                                                                         !          !  !  !     +-9 
  STIGRGRG--------MC------LT--EC--STKG----TTNA------MGRTSC--------   L   !          !  !  !     ! !   +5t2n_A    
                                                                         !          !  !  !     ! ! +-5 
  ------RA--RG----------RTRG--STRTQGTA------SC----ATMCRGTC--------   L -16          +-14  +----11 +-6 +5t2h_A    
                                                                         !             !        !   ! 
  SCMCRG--RG--------------YT--ST--ECTT------RG----TTRG------------   L   !             !        !   +5thg_A    
                                                                         !             !        !  
  CGRGST--------------TTKARG--QTFAQGNG----HCSC----LAQGRGQA--------   L   !             !        +-4yit_A    
                                                                         !             !  
  YCSTTC------------KG----YC--TGET--EC----RG--RG--MA--RGRG--------   L   !             +---------3uvf_B    
                                                                         !  
  --YT--------------------RGSGECRGVTTGQG--VG------RTEARGSC--------   L   +-----------------------2vs7_A    
                                                                       


> 1tc3_C:TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS

  
  RT----HGSGRGHG--RT----   L                         +1tc3_C    
                                      +--------------1 
  --RTQG----PTSGTCSTTC--   L     +----2              +1hlv_A    
                                 !    ! 
  ------------NG----NA--   L   +-3    +---------------2kdz_A    
                               ! ! 
  NG------STHG--CTSTKG--   L --4 +--------------------1pdn_C    
                               ! 
  ----------YTVC--KGDCKC   L   +----------------------2qhb_A    
                             


> 1tez_B:COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

  
  --RT--------ETWTYT------------PA--------                 +-1tez_B    
                                                   +-------2 
  --------------------------SCQC--FARG----         !       ! +6fn0_A    
                                                 +-3       +-1 
  --------------------------HCQC--FCRG----   L   ! !         +2wq7_A    
                                               --4 ! 
  HGRTNT----ET--WT--YTMT--WT--------RT----   L   ! +---------2xrz_B    
                                                 ! 
  --RT--WTFT--ETWT------NT------ETDTRTYTHT   L   +----------2vtb_A    
                                               


> 1tf6_A:CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

  
  KG--WTKA--------HCHG--RGTA--ACNAKGRGLTSTRG--RG   L              +---------------1tf6_A    
                                                                  ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG------------   L              !                +5kl3_A    
                                                                  !              +-1 
  KT--STHT----RG--DAQA--RGRGSTDCHGTT------------   L              !              ! +6b0o_A    
                                                                +-7            +-3 
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG------------   L            ! !            ! ! +1g2f_F    
                                                                ! !       +----4 +-2 
  RG--DCHG--------KGDC--RGQARGATNA--------------   L            ! !       !    !   +2i13_A    
                                                                ! !   +---5    ! 
  EC--SCKGRG----TCYCKA--RGQA----TC--------------   L   +--------8 !   !   !    +--5yeg_A    
                                                       !        ! +---6   ! 
  ----TTSGRG------ECYC----NTYGQGFT--------------   L   !        !     !   +-------5vmy_A    
                                                       !        !     ! 
  CT--STQTLTITST--STHT--RGRG----EARA------------   L --9        !     +-----------5v3j_F    
                                                       !        ! 
  ------------RG--DGEC--RGRGSGDCHA--------------   L   !        +-----------------2wbs_A    
                                                       ! 
  ------TG----RA--SCDC----------------QG--LGLC--   L   +--------------------------5yel_A    
                                                     


> 1u8r_B:CRYSTAL STRUCTURE OF AN IDER-DNA COMPLEX REVEALS A CONFORMATIONAL CHANGE IN ACTIVATED IDER FOR BASE-SPECIFIC INTERACTIONS

  
  ------------ST--PTTC--STQC----RC------------   L                     +----------1u8r_B    
                                                                 +----16  
  ------------ST--PTTC----QG----RG------------   L               !     +----------1f5t_A    
                                                                 !  
  ------------TT--PTTC--STNT------------------   L               !                +4lln_I    
                                                                 !              +-7 
  ------------DCSA--TA--TT------RT------------   L            +-18              ! ! +1z9c_A    
                                                              !  !              ! +-3 
  ------------LTRTPTNA--VT--------------------   L            !  !   +----------8   +6c2s_D    
                                                              !  !   !          ! 
  --------------RGTCTA----RGNT----------------   L            !  !   !          ! +4fx4_B    
                                                              !  !   !          +-5 
  --------------RGSTRT--STHG------------------   L            !  +--17            +3zpl_B    
                                                              !      !  
  ------TT--------KATT--QTTG--LTRTKA------FTYT   L            !      !        +---2p7c_B    
                                                              !      !   +----9 
  ------------STPTATAT--TTKG------------------   L            !      +--13    +---5yi2_J    
                                                        +----19          !  
  ------------STQASGAT--STQT------------QA----   L      !     !          +--------4on0_B    
                                                        !     !  
  RC--------------RGRG--YC--------------------   L      !     !             +---1cf7_A    
                                                        !     !          +-10  
  ------ST----STQAQGST--SART------------------   L      !     !     +---12  +---5trd_B    
                                                        !     !     !    !  
  ------------STKTPTTT--FT--------------------   L      !     !     !    +-----4aso_F    
                                                        !     !     !  
  ----------------------------YG--------------          !     !     !            +2heo_D    
                                                        !     +----15          +-1 
  ----------------------------YGRG------------       +-20           !          ! +4wcg_B    
                                                     !  !           !     +----6 
  ----------------------------YG--------------       !  !           !     !    !   +4ka4_B    
                                                     !  !           !     !    ! +-2 
  ----------------KGTA----TA----RG------------   L   !  !           +----11    +-4 +1xsd_A    
                                                     !  !                 !      ! 
  --------SGQG--YCNC--------------------------       !  !                 !      +2ve9_C    
                                                   -21  !                 !  
  --------RG--STRGMCTT--RT--------------------   L   !  !                 +----4u0y_B    
                                                     !  !  
  ------------QTPTPG--TTRG------------HT------   L   !  !            +---------5xxp_A    
                                                     !  +-----------14  
  ----------------QC--------------------------       !               +---------5hso_A    
                                                     !  
  --KAFA----------------------------FGMC------       +------------------------3aaf_B    
                                                   


> 1uaa_B:E. COLI REP HELICASE/DNA COMPLEX

  
  ----HTDTKTRTATFTLTDTQTFT----WTRTRTHTHTSTST------   L                    +----------1uaa_B    
                                                             +------------2 
  FT--HT------------ST--FT----WGRTRTHGSTMT--RTEGEG           !            !     +----2is6_B    
                                                         +---3            +-----1 
  FTTTHT----------------FTDTYTWTRTRT--------------   L   !   !                  +----2pjr_A    
                                                       --4   ! 
  ----------------------------VT----HT------------   L   !   +-----------------------3gpl_A    
                                                         ! 
  ----------------------------------------------EG   L   +---------------------------5o6b_B    
                                                       


> 1ubd_C:CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT

  
  KT--STHT----RG--DAQA--RGRGSTDCHGTTRG--DAEGRG   L                     +--6b0o_A    
                                                     +-----------------2 
  CT--STQTLTITST--STHT--RGRG----EARA--TTTGECRG   L   !                 +--5v3j_F    
                                                     ! 
  ----KGDCRG--QARGATNA----QA--ATHG--RG--DCNATT   L   !           +--------2i13_A    
                                                     !     +-----4 
  ------KGRG----TCYCKA--RGQA----TC--RA--SCDCVT   L --8     !     +--------5yeg_A    
                                                     !     ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG----------   L   !   +-6              +5kl3_A    
                                                     !   ! !       +------1 
  KG----KA--------HCHG--RGTA--ACNAKG----------   L   !   ! !    +--3      +1tf6_A    
                                                     !   ! !    !  ! 
  ----------STQAQTATSTNTATTTLAHGTCRG----------   L   +---7 +----5  +------1g2f_F    
                                                         !      ! 
  ----TTSGRG------ECYC----NTYGQGFT------------   L       !      +---------5vmy_A    
                                                         ! 
  ------------------------RG--DGECRGRGSGDCHA--   L       +----------------2wbs_A    
                                                   


> 1vtn_C:CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF RESEMBLES HISTONE H5

  
  --------------------------NA----RAHT--STLT------------------   L                                         +-----2a07_K    
                                                                                                         +-4 
  --------------------------NAST--RTHT--ST--------------------   L                                     +-5 +-----3l2c_A    
                                                                                                       ! ! 
  --------------------KGTA----TA------RG----------------------   L                                     ! +-------1xsd_A    
                                                                                                   +---7 
  --------SGQG------YCNC--------------------------------------                                     !   !         +2ve9_C    
                                                                                                   !   !       +-1 
  ------TT------------KATT--QTTG----LTRT----KA----------------   L                            +----8   +-------2 +2p7c_B    
                                                                                              !    !           ! 
  ----------------------------------YG------------------------                                !    !           +-4lb5_B    
                                                                                           +-10    ! 
  ------------------RGSTRT--STHG------------------------RA----   L                         !  !    +-------------3zpl_B    
                                                                                           !  !  
  --KAFA--------------------------------------------YA--FGMC--                             !  !    +-------------3aaf_B    
                                                                                           !  +----9 
  --------------STQTPTPG--TTRG--------------------------------   L                      +-11       +-------------5xxp_A    
                                                                                        !  !  
  RC------------------RGRG--YC--------------------------------   L                      !  !              +---1cf7_A    
                                                                                        !  !         +----3 
  ----------------------------------YG------------------------                      +--12  +---------6    +---2heo_D    
                                                                                    !   !            ! 
  ----------------------NG----RGRG----------------------------   L                  !   !            +--------1cf7_B    
                                                                                 +-13   !  
  ------------RT----------------------------------------------   L               !  !   +---------------------5fmf_V    
                                                                              +-14  !  
  --------YC------KTHGSTQT--YTPT----------------------LG------   L            !  !  +-------------------------5x11_A    
                                                                           +-15  !  
  --------------------------------------------RGKG----------YG   L         !  !  +---------------------------5vfx_A    
                                                                        +-16  !  
  --------------------SGTT--TTYC------------------------------   L      !  !  +----------------------------5f7q_C    
                                                                     +-17  !  
  ----------------TT----RT------------------------SGRT--KT----   L   !  !  +----------------------------2v1u_A    
                                                                   -18  !  
  ------------------------ST------------------------------RA--       !  +-----------------------------5bs8_A    
                                                                     !  
  --------------DCKGRGNA--RT--------KT------------------KGRA--   L   +-----------------------------5ddg_A    
                                                                   


> 1w0t_A:HTRF1 DNA-BINDING DOMAIN IN COMPLEX WITH TELOMERIC DNA.



> 1w36_B:RECBCD:DNA COMPLEX



> 1w36_C:RECBCD:DNA COMPLEX

  
  ----HTDT--RTHT----------------   L                           +-----------1uaa_B    
                                             +-----------------3 
  FTTT----DTRT------------------   L       +-4                 +-----------2pjr_A    
                                           ! ! 
  --------------------NCICNARGRG   L     +-5 +-----------------------------6fqp_B    
                                         ! ! 
  --------------------NCITNARGRG   L     ! +-----------------------------6fqq_E    
                                       +-6 
  --------------RT----NT--NAIARG   L   ! !                             +4cyc_B    
                                       ! !                          +--1 
  --------------------NT--NAIARG   L --7 +--------------------------2  +1puf_B    
                                       !                            ! 
  --------------HTRT--NCSTNARG--   L   !                            +--1k61_B    
                                       ! 
  ------------------RTIAQCNA----   L   +-----------------------------5jlw_D    
                                     


> 1wb9_A:CRYSTAL STRUCTURE OF E. COLI DNA MISMATCH REPAIR ENZYME MUTS, E38T MUTANT, IN COMPLEX WITH A G.T MISMATCH

  
  MGDAFGTTRCMC--PT--   L                              +--1wb9_A    
                                                    +-1 
  ----FGET----------                              +-2 +--1ewq_A    
                                                  ! ! 
  --YGKA------SAPA--                           +--3 +----3thx_B    
                                               !  ! 
  VCKCFGET------PG--       +-------------------4  +-----2o8b_B    
                           !                   ! 
  --DGFG------VGSG--     --5                   +--------3thx_A    
                           ! 
  ----------------RT       +----------------------------1jfi_B    
                         


> 1x9m_A:T7 DNA POLYMERASE IN COMPLEX WITH AN N-2- ACETYLAMINOFLUORENE-ADDUCTED DNA

  
  ------------------KT----------RTNGQG------------YA----------------------QA----                         +------------1x9m_A    
                                                                                                         ! 
  --------------------YG--------RGNG--NGRC----YG--YAIGSCYC--NG--RC--------QA--HG                         !            +-4yfu_D    
                                                                                                         !          +-1 
  --LC----MGRCEG----------SGHGVC------------------------------------------------           +-------------5        +-2 +-1kln_A    
                                                                                           !             !        ! ! 
  --------------KC--------------RGNG--NG----TGFG--YGMG----RG--------------QG--HG   L       !             !      +-3 +---4bwj_A    
                                                                                           !             !      ! ! 
  ----------------KA------------RG--NT------QC------MC------QC------------------         +-7             +------4 +----4x0q_B    
                                                                                         ! !                    ! 
  ------------------------------RG--------EG--YGAC--AC----RC------------------HC   L     ! !                    +-----4xvk_A    
                                                                                         ! ! 
  ----------------------EG------------------QG--TGYGVG--------EG------RG--------   L   +-8 !           +--------------4boc_A    
                                                                                       ! ! +-----------6 
  ----------------------------------------------TT--------QG----------------HT--   L   ! !             +--------------1msw_D    
                                                                                     --9 ! 
  ------------------NG----------RT----------IGYG------------------EGMCTCNGQT----       ! +----------------------------4ztu_A    
                                                                                       ! 
  TT--NTFT----------------------------------------------------------------------       +----------------------------2py5_B    
                                                                                     


> 1x9n_A:CRYSTAL STRUCTURE OF HUMAN DNA LIGASE I BOUND TO 5'-ADENYLATED, NICKED DNA

  
  RT--------------------KGTT--FG   L                        +------1x9n_A    
                                             +--------------2 
  ------------------------ST--FG             !              ! +----6bkg_A    
                                       +-----3              +-1 
  YC--------------FT--------RCFG       !     !                +----3l2p_A    
                                     --4     ! 
  --------------FG--LC--KGTA--FC       !     +---------------------6gdr_A    
                                       ! 
  --YALARAKAIAEA------FA--------       +---------------------------2hvr_B    
                                     


> 1xbr_B:T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA

  
  RGTTATFTACFG   L       +6f59_B    
                       +-1 
  RGTTATFT--FG   L   +-2 +1h6f_B    
                     ! ! 
  RGTT--FG--FT     --3 +-5t1j_B    
                     ! 
  RGTTATFG--FG       +-4a04_B    
                   


> 1xo0_B:HIGH RESOLUTION STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION

  
  HTTAECMA--ST------KTTT--QTQT----CTRA--MT----------KA--RARTRCSA--YA--QG------RA------------   L                                  +5u91_B    
                                                                                                                       +----------1 
  HTTTKGMT--ST------KATT----QT------QT--------------KA--RARTKTST--RG--EA------RA------------   L                     +-2          +1xo0_B    
                                                                                                                     ! ! 
  KATT--AAYT--WT--TTKATTQTSTLT--LTNT--ST--LTLT------------------------QA--------DC--KCTC--IC   L             +-------3 +----------2a3v_C    
                                                                                                             !       ! 
  NATA------RT--TT----NA----RASA--------------------------------ATVTDT------RC--NT--------MT   L         +---4       +----------6en1_A    
                                                                                                         !   ! 
  ------------------------------------------------------------TTQAATYGYAKT------------------   L      +--5   +------------------5jk0_B    
                                                                                                      !  ! 
  --------------------------------------------FCKC----KC----------NT--RGSTKT----------------   L   +--6  +----------------------1flo_A    
                                                                                                   !  ! 
  ------------------------------------------------KTDA------------------TT------------------   L --7  +-------------------------2b9s_A    
                                                                                                   ! 
  ------------------------------------------------------------------------------NGRG--TTRGKT   L   +----------------------------5ds9_A    
                                                                                                 


> 1xpx_A:STRUCTURAL BASIS OF PROSPERO-DNA INTERACTION; IMPLICATIONS FOR TRANSCRIPTION REGULATION IN DEVELOPING CELLS



> 1xsd_A:CRYSTAL STRUCTURE OF THE BLAI REPRESSOR IN COMPLEX WITH DNA

  
  --------------------KGTA----TA----RG------------------   L                 +------------1xsd_A    
                                                                             !  
  --------TT----------KATT--QTTG--LTRT----KA------FT--YT   L                 !        +----2p7c_B    
                                                                          +-18  +-----9 
  ----------------STPTATAT--TTKG------------------------   L              !  !  !     +----5yi2_J    
                                                                          !  !  !  
  ----------------LTRTPTNA--VT--------------------RT----   L              !  +-15         +-6c2s_D    
                                                                          !     !       +-7 
  ------------------RGSTRT--STHG------------------RA----   L              !     !    +--8 +-3zpl_B    
                                                                          !     !    !  ! 
  ----------------TT--PTTC--STNT------------------RT----   L          +--19     +---10  +--4lln_I    
                                                                      !   !          !  
  ------------------SANCTG--TTPT------------------RT----   L          !   !          +-----5hlg_E    
                                                                      !   !  
  --------------------------------YG--------------------              !   !              +4lb5_B    
                                                                      !   !       +------3 
  ----------------DCSA--TA--TT------RT------------RA----   L          !   !   +--13      +1z9c_A    
                                                                      !   !   !   !  
  ----------------STKTPTTT--FT----------------RA--------   L          !   +--16   +-------4aso_F    
                                                                      !       !  
  --------ST------STQAQGST--SART------------KT----------   L          !       +-----------5trd_B    
                                                                   +-21  
  ----------SG--QG--YCNC--------------------------------           !  !                    +2ve9_C    
                                                                   !  !          +---------2 
  LAHAKARA------------------------------------------IAVA           !  !          !         +6dta_A    
                                                                   !  !          !  
  --------------------------------YG--------------------           !  !          !            +4ka4_B    
                                                                   !  !          !          +-4 
  --------------------------------YGRG------------------           !  !       +-14          ! +4wcg_B    
                                                                   !  !       !  !        +-5 
  --------------------------------YG--------------------           !  !       !  !        ! ! +2heo_D    
                                                                   !  !       !  !   +----6 +-1 
  --------------------RGRG--YC--------------------------   L   +--22  !       !  !   !    !   +1cf7_A    
                                                               !   !  +------17  +--11    ! 
  ----------------ST--PTTC----QG----RG------------------   L   !   !          !      !    +1f5t_A    
                                                               !   !          !      !  
  ----------------QTPTPG--TTRG--------------HT----------   L   !   !          !      +-----5xxp_A    
                                                               !   !          !  
  ------------RG--STRGMCTT--RT--------------------------   L   !   !          +-----------4u0y_B    
                                                             -23   !  
  --------------------------NA--RAHT--STLT--------------   L   !   !               +------2a07_K    
                                                               !   !   +----------12  
  --------------------------NASTRTHT--ST----------------   L   !   +--20           +------3l2c_A    
                                                               !       !  
  ----------YC----KTHGSTQT--YTPT----------------LG------   L   !       +------------------5x11_A    
                                                               !  
  --------------------DCKT----RG--RGYA------------------   L   +--------------------------1dux_F    
                                                             


> 1yo5_C:ANALYSIS OF THE 2.0A CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX OF HUMAN PDEF ETS DOMAIN BOUND TO THE PROSTATE SPECIFIC ANTIGEN REGULATORY SITE

  
  ------KT--RGSA--RGQA--------RA   L                           +1yo5_C    
                                                             +-3 
  ------KT--RGAT--RGYA----------   L                         ! +1bc8_C    
                                                    +--------5 
  ----DCKT--RG----RGYA----------   L                !        ! +1dux_F    
                                                    !        +-1 
  ------KT--RGAT--RGYT----------   L          +-----6          +1awc_A    
                                              !     ! 
  KTHG--------------------------              !     !          +5hdn_C    
                                           +--7     +----------2 
  ------ST--------RTQT--MT------   L       !  !                +5d8k_B    
                                           !  ! 
  ----KG----ATNT--CT----SC------   L   +---8  !               +2irf_L    
                                       !   !  +---------------4 
  ------------NT--CT--NGST------   L   !   !                  +1if1_B    
                                     --9   ! 
  --------NA----RAHT--STLT------   L   !   +-------------------2a07_K    
                                       ! 
  ------------------------KGKG--   L   +-----------------------5xfr_B    
                                     


> 1z19_B:CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE(75-356) DIMER BOUND TO A COC' CORE SITE

  
  KGTA--NAYASG--ATST----LT----------------------------------KT--RCST----TTSTRGYC----TT--QT   L                      +-------1z19_B    
                                                                                                                  +-1 
  KATT--AAYT--WT--TTKATTQTSTLT--LTNT----ST--LTLTITFTRT------KA------------QA------DCKCTCIC   L             +------2 +-------2a3v_C    
                                                                                                           !      ! 
  NATA------RT--KTTT----NA----RASA--------YT------------------------ATVTDT--------NT--MT--   L           +-3      +---------6en1_A    
                                                                                                         ! ! 
  HTTAECMA--ST--------KTTT--QTQT----CTRA------------------KA------SA--YA--QG--------------   L       +---4 +----------------5u91_B    
                                                                                                     !   ! 
  --------------AATA--KGNA----IT----------------------------------TTQAATYGYAKT--------TT--   L   +---5   +------------------5jk0_B    
                                                                                                 !   ! 
  ----------------------------------------------------RAFC--KC--------NT--RGST--KT--------   L --6   +----------------------1flo_A    
                                                                                                 ! 
  ----------------------------------------------------------KTDA------TT------------------   L   +--------------------------2b9s_A    
                                                                                               


> 1z63_B:SULFOLOBUS SOLFATARICUS SWI2/SNF2 ATPASE CORE IN COMPLEX WITH DSDNA

  
  ------RC------                  +-----------------1z63_B    
                           +------2 
  ----------NT--   L       !      !         +-------5vvr_M    
                         +-4      +---------1 
  ----EG--------         ! !                +-------6ftx_W    
                       +-5 ! 
  ------------NA   L   ! ! +------------------------3v4r_B    
                       ! ! 
  ------------QA   L --6 +--------------------------4qqw_A    
                       ! 
  --RG--QCQC----   L   !        +------------------5n8r_B    
                       +--------3 
  RAYTEC--------                +------------------2p6r_A    
                     


> 1z9c_A:CRYSTAL STRUCTURE OF OHRR BOUND TO THE OHRA PROMOTER: STRUCTURE OF MARR FAMILY PROTEIN WITH OPERATOR DNA

  
  ------DCSA--TATT------RT----RA------   L                        +1z9c_A    
                                                                +-2 
  ------LTRTPTNAVT------------RT------   L                +-----6 +6c2s_D    
                                                          !     ! 
  ------TT--PTTCSTNT----------RT------   L                !     +-4lln_I    
                                                      +--11  
  --------RGTCTA--RGNT--------RT------   L            !   !      +4fx4_B    
                                                      !   !   +--3 
  --------RGSTRTSTHG----------RA------   L            !   +---8  +3zpl_B    
                                             +-------15       ! 
  --------SANCTGTTPT----------RT------   L   !        !       +---5hlg_E    
                                             !        !  
  ----------QC------------------------       !        !  +--------5hso_A    
                                             !        +-12  
  ------STPTATATTTKG------------------   L   !           +--------5yi2_J    
                                             !  
  ------STKTPTTTFT------------RA------   L   !                 +-----4aso_F    
                                           -19             +--10  
  ------STQASGATSTQT----------QA------   L   !       +----13   +-----4on0_B    
                                             !       !     !  
  ST----STQAQGSTSART--------KT--------   L   !    +-17     +---------5trd_B    
                                             !    !  !  
  ------ST--PTTC--QG----RG------------   L   !    !  +---------------1f5t_A    
                                             !    !  
  TT--------KATTQTTG--LTRTKA------FTYT   L   !    !          +----2p7c_B    
                                             +---18  +-------9 
  --------------------YG--------------            !  !       !   +4lb5_B    
                                                  !  !       +---4 
  ----------KGTA--TA----RG------------   L        !  !           +1xsd_A    
                                                  !  !  
  --SGQG--YCNC------------------------            +-16         +--2ve9_C    
                                                     !  +------7 
  --------------------YG--------------               !  !      ! +4ka4_B    
                                                     !  !      +-5 
  --------------------YG--------------               +-14        ! +2heo_D    
                                                        !        +-1 
  --------------------YGRG------------                  !          +4wcg_B    
                                                        !  
  ------STQTPTPGTTRG------------HT----   L              +---------5xxp_A    
                                           


> 1zlk_A:CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR C-TERMINAL DOMAIN-DNA COMPLEX

  
  ------KGTGKANGYAST------   L                                 +1zlk_A    
                                                           +---1 
  ------KGTCKGTCHT--------   L                    +--------4   +4wuh_B    
                                                  !        ! 
  ----ITKGTASTSAQT--------   L            +-------9        +---5w43_B    
                                          !       ! 
  ------SCTAKTVCHTKG------   L            !       !     +------1je8_F    
                                       +-11       +-----6 
  --STQTPTPGTTRG----------   L         !  !             +------5xxp_A    
                                       !  !  
  ------RG--DTVT--STRG----   L         !  +--------------------4nhj_A    
                                       !  
  TT----KATTQTTG----LTRTKA   L      +-12                 +---2p7c_B    
                                    !  !             +---3 
  --STPTATATTTKG----------   L      !  !       +-----7   +---5yi2_J    
                                    !  !       !     ! 
  --LTRTPTNAVT------------   L      !  !       !     +-------6c2s_D    
                                    !  !       !  
  ----SANCTG--TTPT--------   L      !  +------10        +----5hlg_E    
                                 +-13          ! +------5 
  ----RGTCTA--RGNT--------   L   !  !          ! !      !   +4fx4_B    
                                 !  !          +-8      +---2 
  --DCSA--TATT--------RT--   L   !  !            !          +1z9c_A    
                               -14  !            ! 
  ------------------YG----       !  !            +-----------4ka4_B    
                                 !  !  
  --ST--RG----------------   L   !  +------------------------2qby_B    
                                 !  
  ----YTNT--RGVT--RTET----   L   +---------------------------1l3l_A    
                               


> 1zq3_P:NMR SOLUTION STRUCTURE OF THE BICOID HOMEODOMAIN BOUND TO THE CONSENSUS DNA BINDING SITE TAATCC



> 1zrf_A:4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6C;17G]ICAP38 DNA

  
  --QT--STRGEC----RG--   L                              +1zrf_A    
                                                      +-1 
  ------HT--STATSTRG--   L                          +-3 +5lej_A    
                                                    ! ! 
  ------STRGECTANGKG--   L       +------------------6 +-3mzh_A    
                                 !                  ! 
  ------ITRGECSCSGKG--   L       !                  ! +--5i2d_R    
                                 !                  +-4 
  ------TTLTECTASTRG--   L       !                    +--4i2o_B    
                             +---9 
  --RG--STRGMCTTRT----   L   !   !              +-------4u0y_B    
                             !   !            +-7 
  ----------RGRGYC----   L   !   !            ! +-------1cf7_A    
                             !   +------------8 
  ------------------YG     -10                !         +2heo_D    
                             !                !      +--2 
  --SGQG--YCNC--------       !                +------5  +2ve9_C    
                             !                       ! 
  ------------------YG       !                       +--4lb5_B    
                             !  
  RT------------------   L   +--------------------------5vfx_A    
                           


> 2a07_K:CRYSTAL STRUCTURE OF FOXP2 BOUND SPECIFICALLY TO DNA.

  
  --------------------------------NA----RAHT--STLT------------------   L                                  +-----2a07_K    
                                                                                                       +-11  
  --------------------ST----------NAST--RTHT--ST--------------------   L                         +----13  +-----3l2c_A    
                                                                                                 !     !  
  --------KAFA----------------------------------------YANAKTFGMC----                             !     +--------3aaf_B    
                                                                                              +-17  
  ------------TT------------KATT--QTTG----LTRT----KA------------FTYT   L                      !  !            +-2p7c_B    
                                                                                              !  !    +-------7 
  --------------------------KGTA----TA------RG----------------------   L                      !  +---14       +-1xsd_A    
                                                                                              !       !  
  ----------------------RGSTRT--STHG------------------------RA------   L                      !       +---------3zpl_B    
                                                                                              !  
  --------------------STKTPTTT--FT--------------------------RA------   L               +-----19         +--------4aso_F    
                                                                                       !      !  +-----12  
  ----------------------------------------YG------------------------                   !      !  !      !       +4lb5_B    
                                                                                       !      !  !      +-------3 
  ------------ST--------STQAQGST--SART------------------------------   L               !      !  !              +5trd_B    
                                                                                       !      !  !  
  --------------SGQG----YCNC----------------------------------------                   !      !  !               +2ve9_C    
                                                                                       !      +-18             +-2 
  --LAHAKARA--------------------------------------------------------                   !         !             ! +6dta_A    
                                                                                    +-21         !          +--6 
  ----------------------------------------YG------------------------                !  !         !          !  ! +4ka4_B    
                                                                                    !  !         !     +----9  +-5 
  ----------------------------------------YG------------------------                !  !         !     !    !    +2heo_D    
                                                                                    !  !         +----15    ! 
  RC------------------------RGRG--YC--------------------------------   L            !  !               !    +----1cf7_A    
                                                                                 +-23  !               !  
  ------------------RT----------------------------------------------   L         !  !  !               +---------5fmf_V    
                                                                                 !  !  !  
  --------------YC------KTHGSTQT--YTPT------------------------------   L         !  !  +------------------------5x11_A    
                                                                                 !  !  
  ----------------------------------------------------KG------------   L         !  !  +-----------------------5xfr_B    
                                                                                 !  +-20  
  --------------------NG----RGRG--YC--------------------------------   L      +-24     +-----------------------1cf7_B    
                                                                              !  !  
  ----------------------------KT----RGAT--RGYA----------------------   L      !  !                         +--1bc8_C    
                                                                              !  !                 +-------8 
  ----------------------------KT----RG----RGYA----------------------   L      !  !                 !       ! +1dux_F    
                                                                              !  !  +-------------16       +-4 
  ----------------------------KT----RGSA--RGQA----------------RA----   L      !  !  !              !         +1yo5_C    
                                                                           +-25  +-22              !  
  ----------------------------------NT--RGCT--NGST------------------   L   !  !     !              +----------1if1_B    
                                                                           !  !     !  
  --------------------------------------------------RGKG----NT--YG--   L   !  !     +-------------------------5vfx_A    
                                                                           !  !  
  --------------------------AA----ET------------------------RG------   L -26  !                       +----5eix_A    
                                                                           !  +----------------------10  
  --------------------------SG--------------------------------------       !                          !    +5iwi_C    
                                                                           !                          +----1 
  --------------------------SA--------------------------------------   L   !                               +5npk_d    
                                                                           !  
  ------------------------------------------------------TGAG--ATTT--       +----------------------------2wwy_B    
                                                                         


> 2a3v_C:STRUCTURAL BASIS FOR BROAD DNA-SPECIFICITY IN INTEGRON RECOMBINATION

  
  KATT--AAYT--WTTTKATTQTSTLTLTNT--ST--LTLTITFTRTSTKA----------------QA--DCKCTCIC   L              +----------2a3v_C    
                                                                                                +-1 
  HTTAECMA--ST----KTTT--QTQT--CTRA--MT--------------RARTRC--SA--YA--QG----------   L   +--------2 +----------5u91_B    
                                                                                       !        ! 
  NATA------RT----KTTT----NA--RASA------------------------DT----------RCNT--MT--   L --3        +-----------6en1_A    
                                                                                       ! 
  ----------------AATA--KGNA--IT----------------------------TTQAATYGYAKT----TT--   L   +--------------------5jk0_B    
                                                                                     


> 2b9s_A:CRYSTAL STRUCTURE OF HETERODIMERIC L. DONOVANI TOPOISOMERASE I- VANADATE-DNA COMPLEX

  
  KANT--RGMGYAMCKT--NC--KTDA------TT--   L                             +2b9s_A    
                                                    +------------------1 
  ----ECRA--YAMCKT--NT--KT------------       +------3                  +1k4t_A    
                                             !      ! 
  ----------------RG--------RG--------   L --4      +-------------------3m4a_A    
                                             ! 
  --------------------KA------QG------   L   !         +----------------5u91_B    
                                             +---------2 
  ----------------------------TTQAYAKT   L             +----------------5jk0_B    
                                           


> 2bcq_A:DNA POLYMERASE LAMBDA IN COMPLEX WITH A DNA DUPLEX CONTAINING AN UNPAIRED DTMP

  
  WC--LC----KA--YCAGNGRCRGEGKTPT                      +--2bcq_A    
                                                    +-2 
  --SALTAART------RGEGRGRG------                    ! +--4qz9_A    
                                          +---------3 
  HC--------KG--YCDCNCKGRG------          !         ! +-4kli_A    
                                          !         +-1 
  ----LC--RCRAFT--KTQTRARA------       +--5           +-5vzi_A    
                                       !  ! 
  --------------YA--------------       !  !  +---------3v7j_A    
                                     --6  +--4 
  ----------KC----KA--VARA------       !     +---------4p4m_A    
                                       ! 
  ----------KT--HCVGLCIGRG------       +---------------5hrb_A    
                                     


> 2bop_A:CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET

  
  ------KGCGFT------------------   L                        +-----2bop_A    
                                                      +-----2 
  --KTTGYCNGRT------------------   L                  !     +-----1b3t_A    
                                         +------------3 
  ----NCKGCAYGRA----------------   L     !            !           +2ayg_A    
                                       +-4            +-----------1 
  ----------------------------WG       ! !                        +6dgd_B    
                                     --5 ! 
  --------------------------RG--   L   ! +------------------------3qfq_B    
                                       ! 
  KG------------NTECKCDGHGYT----   L   +-------------------------1lwt_A    
                                     


> 2bzf_A:STRUCTURAL BASIS FOR DNA BRIDGING BY BARRIER-TO- AUTOINTEGRATION FACTOR (BAF)



> 2c6y_A:CRYSTAL STRUCTURE OF INTERLEUKIN ENHANCER-BINDING FACTOR 1 BOUND TO DNA

  
  ------------------------NASTRGHT--STLT----------------KA------   L                                   +---2c6y_A    
                                                                                              +-------10  
  ------------------------NASTRGHT--STFT------------------------   L                          !        !   +1vtn_C    
                                                                                         +---16        +---1 
  --------------TT----RT----------------------SG--RT----KT------   L                     !    !            +2v1u_A    
                                                                                      +-18    !  
  --------------TT--RG----ST----------------------------KT------   L                  !  !    +------------2qby_A    
                                                                                      !  !  
  ------YC------KTHGSTQT--YTPT------------------------LG--------   L                  !  +-----------------5x11_A    
                                                                                      !  
  ------------------------NASTRGHT--STFT------------------------   L                  !                      +--5x07_F    
                                                                                      !                 +----7 
  ------------------------NA--RAHT--STLT------------------------   L                  !        +-------12    +--2a07_K    
                                                                                      !        !        !  
  ----------------------------------------KGKG------------------   L                  !        !        +-------5xfr_B    
                                                                                      !        !  
  ------------------------NASTRTHTNTSTLT------------------------   L                  !        !                +3co6_C    
                                                                                   +-21     +-17       +--------2 
  ----------ST------------NASTRTHT--ST--------------------------   L               !  !     !  !   +--13        +3l2c_A    
                                                                                   !  !     !  !   !   !  
  ----------------RGSTRT--STHG--------------------------RA------   L               !  !     !  !   !   +--------3zpl_B    
                                                                                   !  !     !  +--15  
  ------------------------------YG------------------------------                   !  !     !      !           +4lb5_B    
                                                                                   !  !  +-19      !         +-5 
  ----TT------------KATT--QTTG--LTRT----KA--------------------FT   L               !  !  !  !      !         ! +2p7c_B    
                                                                                   !  !  !  !      +---------8 
  ------SGQG------YCNC------------------------------------------                   !  !  !  !                !  +2ve9_C    
                                                                                +-23  !  !  !                +--3 
  ------------------KGTA----TA----RG----------------------------   L            !  !  +-20  !                   +1xsd_A    
                                                                                !  !     !  !  
  KAFA--------------------------------------------YANA--FGMC----                !  !     !  +------------------3aaf_B    
                                                                                !  !     !  
  ------------------RGRG--YC------------------------------------   L            !  !     !             +-----1cf7_A    
                                                                                !  !     +------------11  
  --------------STRGMCTT--RT------------------------------------   L         +-24  !                   +-----4u0y_B    
                                                                             !  !  !  
  --------------STKTPTTT--FT----------------------------RA------   L         !  !  !            +----------4aso_F    
                                                                             !  !  !  +--------14  
  ------------ST--PTPG--TTRG------------------------------HT----   L         !  !  +-22         +----------5xxp_A    
                                                                             !  !     !  
  --------------RT----------------------------------------------   L      +-25  !     +--------------------5fmf_V    
                                                                          !  !  !  
  ------------------------------------------RG--KG----------YG--   L      !  !  +-------------------------5vfx_A    
                                                                          !  !  
  --------------------SA--------------------------------RG------   L      !  !                      +---5npk_d    
                                                                       +-26  +----------------------9 
  --------------------SG--------------------------------RT------       !  !                         !  +5iwi_C    
                                                                       !  !                         +--4 
  --------------------AA----ET--------------------------RG------   L   !  !                            +5eix_A    
                                                                     -27  !  
  --------------------DCKGRGNARTKT--------------------KGRA------   L   !  !                          +-5ddg_A    
                                                                       !  +--------------------------6 
  --------------------QC--KGSGRTRG------------------------------   L   !                             +-3gz6_A    
                                                                       !  
  ------------------------------------RG------------------------       +----------------------------4hly_B    
                                                                     


> 2c7a_B:STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX

  
  ----EC--KA--RGRG----   L   +---------------------4nqa_I    
                             !  
  --------KGVT--RG--RC   L   !                              +2c7a_B    
                             !                            +-4 
  --------KGVT--RG----   L   !                            ! ! +5cbz_E    
                             !                          +-6 +-1 
  ----EC--KG--KGRG----   L   !                          ! !   +1dsz_B    
                             !                          ! ! 
  ----EA--KG--RTRTRT--       !                          ! +2han_B    
                             !                       +-10  
  --HGECAGKGAAKGRT----   L   !                       !  !   +1lo1_A    
                           -16                       !  ! +-8 
  ----EC--KG--KGRA----   L   !                       !  +-9 +5l0m_A    
                             !                    +-13    ! 
  ----EC--KG--KGRG----   L   !                    !  !    +2ff0_A    
                             !                    !  !  
  --------KAVA--RA----   L   !                    !  !  +5e69_A    
                             !                 +-14  +--2 
  ----EC--KG--RGRG----   L   !                 !  !     +2nll_B    
                             !                 !  !  
  --HC----KGVT--RG--RT       !                 !  !  +-3g9m_B    
                             !                 !  !  !  
  ----DG--KG--RTRG----   L   !                 !  +-11   +3cbb_A    
                             +----------------15     ! +-3 
  CA--EC--KG--KGRG----   L                     !     +-7 +1cit_A    
                                               !       ! 
  ----EA--KG--RTRG----   L                     !       +1kb2_B    
                                               !  
  --HAEC--KG--RGRG----   L                     !  +-1a6y_A    
                                               +-12  
  ----ET--KGAT--RG----   L                        ! +1lat_A    
                                                  +-5 
  --------KGVT--RG----                              +5emc_A    
                           


> 2d5v_B:CRYSTAL STRUCTURE OF HNF-6ALPHA DNA-BINDING DOMAIN IN COMPLEX WITH THE TTR PROMOTER



> 2dgc_A:GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA

  
  ------NTRTATATCTRA   L                          +5vpe_D    
                                              +---1 
  RG----NC--YGATCTRG   L                      !   +2wt7_B    
                                            +-5 
  RG--QGNARTAGQTFTRG   L                    ! !    +1gd2_G    
                                            ! !  +-3 
  RC----NC--AAATCTRC   L                    ! +--4 +2wt7_A    
                           +----------------6    ! 
  --RA--NA--AAVTSTRG   L   !                !    +1nwq_C    
                           !                ! 
  ------NCTT--AT--RG   L --7                !    +2dgc_A    
                           !                +----2 
  RG----NC--YGAT--RC   L   !                     +4eot_A    
                           ! 
  ------NG--AT--STRG       +---------------------5szx_B    
                         


> 2dp6_A:CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE IN COMPLEX WITH AP:C CONTAINING DNA

  
  RC--RA--RCQTNT--QGTCRC--   L       +-------------2dp6_A    
                                 +---3 
  --------------PG------NG       !   +-------------1oe4_B    
                               --4 
  --------PALA------------       !               +-4uqm_A    
                                 !            +--1 
  --------PTLT------------       +------------2  +-5nnu_A    
                                              ! 
  --KT--TT----------------                    +----4yig_E    
                               


> 2drp_D:THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION

  
  ------TTSG--RG----ECYC--   L           +--------5vmy_A    
                                   +-----4 
  STQAQTATSTNTATTTLAHGTCRG   L     !     !       +1g2f_F    
                                 +-5     +-------1 
  --RGSTDCHG--TTRG--DAEGRG   L   ! !             +5kl3_A    
                                 ! ! 
  --RG--DGEC--RGRGSGDCHA--   L --6 +--------------2wbs_A    
                                 ! 
  --QA----TC----RA--SCDCVT   L   !        +-----5yeg_A    
                                 +--------3 
  --RGSTDCHG--TTRG--DAEGRG   L            !   +-6b0o_A    
                                          +---2 
  ------KGDC--RGQARGATNA--   L                +-2i13_A    
                               


> 2e1c_A:STRUCTURE OF PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR PH1519/DNA COMPLEX

  
  LTAGETSGTTHT--------------------------   L           +-----------------2e1c_A    
                                               +-------2 
  --------------TAFCSG--------LATGSGVGFA   L   !       !        +--------5tkz_B    
                                             --3       +--------1 
  --------------------KTTGYCNG----------   L   !                +--------1b3t_A    
                                               ! 
  ------------YG------------------------       +-------------------------2heo_D    
                                             


> 2e42_A:CRYSTAL STRUCTURE OF C/EBPBETA BZIP HOMODIMER V285A MUTANT BOUND TO A HIGH AFFINITY DNA FRAGMENT

  
  RG--QGNARTAGQT----FTRG--------------   L             +1gd2_G    
                                                     +-1 
  --------------RG------NC----YGATCTRG   L      +----3 +2wt7_B    
                                                !    ! 
  --------------RG------NC----YGAT--RC   L      !    +4eot_A    
                                             +--5 
  ----------NTRT--ATAT----CTRA--------   L   !  !   +-5vpe_D    
                                             !  +---4 
  ------RA--NA----AAVT----STRG--------   L --6      ! +1nwq_C    
                                             !      +-2 
  --RC----NC--AAAT----CTRC------------   L   !        +2wt7_A    
                                             ! 
  ----------NCTT----AT------RG--------   L   +--------2dgc_A    
                                           


> 2ex5_A:GROUP I INTRON-ENCODED HOMING ENDONUCLEASE I-CEUI COMPLEXED WITH DNA

  
  SANCSCKGLT----------DAECNATG------RC--KGST--------------DA--QA----QCNT   L                     +-------2ex5_A    
                                                                                                 !  
  SAYCLCITRGDCYA--QG--------IG--NA--RG------RG--DTIC--RG----------------   L             +------10    +--2fld_B    
                                                                                         !       !    ! 
  STITQAKGRG--STNTQT--ST--ATTC------------YT--SC--VCDTRG--ST----KGTG----   L             !       +----8    +3mxb_B    
                                                                                         !            !  +-1 
  SGIGQAKGNC--SC--RG--QG--DGTA--YC--------AT--SC--VCKGRG----------TT----   L             !            +--2 +6fb0_A    
                                                                                         !               ! 
  SGIGQAKG----SC--KG------KGTA------------YC--ST--VG--YA--------KCTG----   L             !               +6fb0_B    
                                                                                         !  
  CTFTSTYAST--KTSTAT--QA--KTTG--RA--ET----RG------ATDT----TA------------   L             !                  +4lq0_A    
                                                                               +--------12                +-4 
  SAKGIGKT----SGITQA--IA--QATC------EC----DT--RG--WTYC----TC------------   L   !         !              +-6 +4lox_A    
                                                                               !         !              ! ! 
  CTSTVAFTST--TCSCAT--KA--ITTC------ST------DA--RGTC--KT--TG------------   L   !         !              ! +5esp_A    
                                                                               !         !            +-7 
  TTYTHG----------YC--RGRGIT--------QC------------MCHT----TGKT----------   L   !         !            ! !   +5thg_A    
                                                                               !         !            ! ! +-3 
  HC--NAKT--------YA----RG--SA----RT--KG--KG----FTWTECET--TT------------   L -13         !     +------9 +-5 +5t2h_A    
                                                                               !         !     !      !   ! 
  HT--NCWCRG----------QG----ST--YG--LA--KG--RG--LTWC--RG--TG------------   L   !         !     !      !   +5t2n_A    
                                                                               !         +----11      ! 
  CCMT--ACST--AT--QA--YA--ICTA--RT------------KGRTVAEC--QT--------------   L   !               !      +--4yit_A    
                                                                               !               !  
  CCSTYG------NT--YT--ITSTDT--AT--------YA------TTCCRTKT--TA------------   L   !               +---------3uvf_B    
                                                                               !  
  --YT------------RGSGECRGVTTG--------QG--VG------RTEARG--SC------------   L   +-------------------------2vs7_A    
                                                                             


> 2f8n_G:2.9 ANGSTROM X-RAY STRUCTURE OF HYBRID MACROH2A NUCLEOSOMES



> 2fdc_B:STRUCTURAL BASIS OF DNA DAMAGE RECOGNITION AND PROCESSING BY UVRB: CRYSTAL STRUCTURE OF A UVRB/DNA COMPLEX

  
  ----SGYGYGQCPCYCFCMAFASAICECLCQAMGRG----FT--                                  +--2fdc_B    
                                                         +----------------------1 
  --------YT--PTYT--------------QTMGRT--NAFALA   L     +-2                      +--3v4r_B    
                                                       ! ! 
  --------------------------------------RT----   L   +-3 +-------------------------5vvr_M    
                                                     ! ! 
  FTTT--------------------------------RT------   L --4 +---------------------------2pjr_A    
                                                     ! 
  ------------------------------DA------QA----   L   +----------------------------4qqw_A    
                                                   


> 2ff0_A:SOLUTION STRUCTURE OF STEROIDOGENIC FACTOR 1 DNA BINDING DOMAIN BOUND TO ITS TARGET SEQUENCE IN THE INHIBIN ALPHA- SUBUNIT PROMOTER

  
  ----EC--KG--KGRG--RCRC   L         +2ff0_A    
                               +-----9 
  ----EC--KG--KGRA--RTRC   L   !     +5l0m_A    
                               !  
  --HGECAGKGAAKGRT--RTRC   L   !     +--1lo1_A    
                               !  +-13  
  CA--EC--KG--KGRG------   L   !  !  +--1cit_A    
                             -16  !  
  ----EC--KG--KGRG------   L   !  !        +-1dsz_B    
                               !  !     +-11  
  ----DG--KG--RTRG------   L   !  !     !  ! +3cbb_A    
                               !  !     !  +-1 
  ----EA--KG--RTRTRT----       !  !     !    +2han_B    
                               !  !     !  
  --------KGVT--RG------   L   +-15     !        +2c7a_B    
                                  !     !      +-5 
  ----EC--KA--RGRG------   L      !  +-12      ! +4nqa_I    
                                  !  !  !    +-7 
  --------KAVA--RA------   L      !  !  !    ! ! +5e69_A    
                                  !  !  !  +-8 +-2 
  --------KGVT--RG------   L      !  !  !  ! !   +5cbz_E    
                                  !  !  !  ! ! 
  --HAEC--KG--RGRG------   L      !  !  !  ! +1a6y_A    
                                  +-14  +-10  
  ----ET--KGAT--RG------   L         !     !   +1lat_A    
                                     !     ! +-3 
  ----EA--KG--RTRG------   L         !     +-4 +1kb2_B    
                                     !       ! 
  ----EC--KG--RGRG------   L         !       +2nll_B    
                                     !  
  --------KGVT--RG------             !  +5emc_A    
                                     +--6 
  --HC----KGVT--RG------                +3g9m_B    
                             


> 2fld_B:I-MSOI RE-DESIGNED FOR ALTERED DNA CLEAVAGE SPECIFICITY

  
  SAYCLCITRGDCYA----QG------IG--NARG----RG--DTIC--RG----------   L                          +--2fld_B    
                                                                                            ! 
  SGIGQAKG----SC----KG----KGTA--------YC--ST--VG--YA----KCTG--   L            +-------------8    +6fb0_B    
                                                                              !             !  +-1 
  SGIGQAKGNC--SC----RGQG--DGTAYC------AT--SC--VCKGRG------TT--   L            !             +--2 +6fb0_A    
                                                                              !                ! 
  STITQAKGRG--STNT--QTST--ATTC--------YT--SC--VCDTRGST--------   L            !                +3mxb_B    
                                                                              !  
  SANCSCKGLT----------DAECNATG----RC----------------DAQA----QC   L   +-------12   +------------2ex5_A    
                                                                     !        !   !  
  ST--NAVTHG--TCNA--ATLCYCECAT----YG--NA--SADCTCKTKGSA--------   L   !        !   !               +4lq0_A    
                                                                     !        !   !             +-3 
  SGMGRGRG----KTYA--LTVT----TT------KT--SC--------RGEC--------   L   !        !   !           +-6 +4lox_A    
                                                                     !        !   !           ! ! 
  STMG--------KGYC--RT--RGVTSA------FC--MC----STQTRGEC--------   L   !        +--11           ! +5esp_A    
                                                                     !            !         +-7 
  STIGRGRG------MC--LTEC--STKG------TT--NA------MGRTSC--------   L   !            !         ! ! +5t2n_A    
                                                                   -13            !         ! +-5 
  SCMCRGRG----------YTST--ECTT----------RG----TTRG------------   L   !            !  +------9   ! +5thg_A    
                                                                     !            !  !      !   +-4 
  ------RARG------RTRGSTRTQGTA----------SC----ATMCRGTC--------   L   !            !  !      !     +5t2h_A    
                                                                     !            +-10      ! 
  CGRG------------KARGQTFAQGNG------HC--SC----LAQGRGQA--------   L   !               !      +--4yit_A    
                                                                     !               !  
  YCST--------------YCTGET--EC--------RG--RG------RGRG--------   L   !               +---------3uvf_B    
                                                                     !  
  --YTLT--------------------------QG--VG------RTEARGSC--------   L   +-------------------------2vs7_A    
                                                                   


> 2fr4_B:STRUCTURE OF FAB DNA-1 COMPLEXED WITH A STEM-LOOP DNA LIGAND

  
  SCYA----YT----YCRC----                           +---2fr4_B    
                               +-------------------2 
  ------------------YA--       !                   !   +3vw3_H    
                             --3                   +---1 
  ----YTYTNTECHT--------       !                       +2fr4_L    
                               ! 
  --------------------RT       +-----------------------4oi8_B    
                             


> 2gli_A:FIVE-FINGER GLI/DNA COMPLEX

  
  --KT--STHT--RG--DAQARG--RGSTDCHG----TT--RG--DAEGRG   L                             +-6b0o_A    
                                                                    +----------------3 
  ITST--STHTRGRG----EARA----TTTGEC----RG--RG----ET--   L            !                +-5v3j_F    
                                                                    ! 
  ------------RGSTDAHARG--RGSTDCHG----TT--RG--DAEGRG   L            !                 +5kl3_A    
                                                                    !              +--2 
  ------------QA--TTNA--STQAQTATST--NTAT--TTLAHGTCRG   L   +--------7              !  ! +1g2f_F    
                                                           !        !          +---4  +-1 
  --QARGATNA--QA--ATHG----RG--DCNA----TT--RGRTDAAT--   L   !        !          !   !    +2i13_A    
                                                           !        !  +-------5   ! 
  ----TCYCKARGQA----TC----RA--SCDC----VT------------   L   !        !  !       !   +---5yeg_A    
                                                         --8        +--6       ! 
  ------TTSGRG----ECYC----NTYGQGFT------------------   L   !           !       +-------5vmy_A    
                                                           !           ! 
  ------------RG--DGECRG--RGSGDCHA------------------   L   !           +---------------2wbs_A    
                                                           ! 
  ------------QG--RGHTMG--QG----LGLC----TTRG--------   L   +---------------------------5yel_A    
                                                         


> 2glo_A:SOLUTION STRUCTURE OF THE BRINKER DNA BINDING DOMAIN IN COMPLEX WITH THE OMB ENHANCER

  
  --RTQG--------PTSGTCSTTC----   L            +--------------------------1hlv_A    
                                              ! 
  RT--------HGSGRGHG--RT------   L         +--4                       +--1tc3_C    
                                           !  !   +-------------------2 
  --------------YTVC--KGDC--KC   L         !  !   !                   +--2qhb_A    
                                           !  +---3 
  ----------------NG----NA----   L       +-5      !                     +2kdz_A    
                                         ! !      +---------------------1 
  --------------DCNA--NA--NTST   L       ! !                            +3zqc_A    
                                       +-6 ! 
  ------RALTPTDCHGTCTCLTHT----   L     ! ! +-----------------------------1j1v_A    
                                     +-7 ! 
  --------LTETTTRAECRCRCQC----   L   ! ! +-----------------------------3n97_A    
                                   --8 ! 
  ----------PTTC--------------   L   ! +-----------------------------6c31_A    
                                     ! 
  ------------TGKG------------   L   +-----------------------------4pxi_B    
                                   


> 2gzk_A:STRUCTURE OF A COMPLEX OF TANDEM HMG BOXES AND DNA

  
  RC--NAFTIA--RG--NC--SALT--YAKTEAKARCFAFTCG--IC--VGAG   L   +----------------2gzk_A    
                                                             ! 
  RT--NTFTMA--RT--NG--SA----YA------------------------   L   !               +4y60_C    
                                                           --5           +---2 
  RC--NTFTMA--RAHGNT--SA----YA------------------------   L   !           !   ! +3f27_D    
                                                             !        +--3   +-1 
  KC--NT--MAMA--EGSAACNT------------------------------   L   !        !  !     +2lef_A    
                                                             +--------4  ! 
  ----------------------------------RGYANTVTFGPGQC--LC   L            !  +----3tq6_B    
                                                                      ! 
  RTTASTYAFALT----PTATST--RA--------------------------   L            +-------5jh0_D    
                                                           


> 2h1k_B:CRYSTAL STRUCTURE OF THE PDX1 HOMEODOMAIN IN COMPLEX WITH DNA



> 2h27_A:CRYSTAL STRUCTURE OF ESCHERICHIA COLI SIGMAE REGION 4 BOUND TO ITS-35 ELEMENT DNA

  
  YG--------TGRGSGFTRG------   L                       +---2h27_A    
                                                   +---1 
  ----TTRTECRCRCQC----------   L   +---------------2   +---6c04_F    
                                   !               ! 
  LTEGTT--ETRCRC------------   L --3               +-------6b6h_F    
                                   ! 
  ------------RTRA--TAEGWANG       +-----------------------2p6r_A    
                                 


> 2h7g_X:STRUCTURE OF VARIOLA TOPOISOMERASE NON-COVALENTLY BOUND TO DNA

  
  HTRA--QAYCYT--------RT------KGKGYGKT------ETRGYG   L                 +-----------2h7g_X    
                                                                    +--1 
  ----MG--YA------KT----------NC----KTDA------TT--   L   +----------2  +-----------2b9s_A    
                                                         !          ! 
  ----------------------RG--------------RG--------   L --4          +--------------3m4a_A    
                                                         ! 
  ------------KTTT--QT--------------------RA------   L   !    +--------------------5u91_B    
                                                         +----3 
  ------------------------FCKC------KC--------NTRG   L        +--------------------1flo_A    
                                                       


> 2h8r_B:HEPATOCYTE NUCLEAR FACTOR 1B BOUND TO DNA: MODY5 GENE PRODUCT



> 2han_A:STRUCTURAL BASIS OF HETERODIMERIC ECDYSTEROID RECEPTOR INTERACTION WITH NATURAL RESPONSE ELEMENT HSP27 GENE PROMOTER

  
  ----EC--KG--KGRG----   L             +1dsz_B    
                                    +--5 
  ----EC--KA--RGRG----   L       +-14  +4nqa_I    
                                 !  !  
  ----EC--KG--RGRG----   L   +--16  +---2nll_B    
                             !   !  
  ----EC--KG--KGRG----   L   !   !    +-2ff0_A    
                             !   +----9 
  ----EC--KG--KGRA----   L   !        +-5l0m_A    
                             !  
  --HGECAGKGAAKGRT----   L   !       +---1lo1_A    
                             !       !  
  ----EA--KG--RTRG----   L -17    +-13    +1kb2_B    
                             !    !  !  +-6 
  ----EA--KG--RTRTRT--       !    !  +-10 +2han_B    
                             !    !     !  
  CA--EC--KG--KGRG----   L   !    !     +-1cit_A    
                             !    !  
  ----DG--KG--RTRG----   L   !    !       +-3cbb_A    
                             +---15     +-8 
  --------KAVA--RA----   L        !     ! ! +5e69_A    
                                  !     ! +-4 
  ----ET--KGAT--RG----   L        !  +-11   ! +1lat_A    
                                  !  !  !   +-1 
  --HC----KGVT--RG----            !  !  !     +3g9m_B    
                                  !  !  !  
  --------KGVT--RG----            +-12  +-5emc_A    
                                     !  
  --------KGVG--RG--RA   L           !   +3g6t_A    
                                     ! +-3 
  --HAEC--KG--RGRG----   L           ! ! +1a6y_A    
                                     +-7 
  --------KGVT--RG----   L             ! +5cbz_E    
                                       +-2 
  --------KGVT--RG----   L               +2c7a_B    
                           


> 2han_B:STRUCTURAL BASIS OF HETERODIMERIC ECDYSTEROID RECEPTOR INTERACTION WITH NATURAL RESPONSE ELEMENT HSP27 GENE PROMOTER

  
  ----EA--KG--RTRTRT----               +-2han_B    
                                     +-8 
  ----EC--KG--RGRG----KA   L         ! +-2nll_B    
                               +----13  
  ----EA--KG--RTRG------   L   !     !  +1kb2_B    
                               !     +--5 
  ----EC--KA--RGRG------   L   !        +4nqa_I    
                               !  
  ----EC--KG--KGRG------   L   !         +-1dsz_B    
                               !       +-9 
  --HGECAGKGAAKGRT------   L -16    +-12 +-1lo1_A    
                               !    !  !  
  CA--EC--KG--KGRG------   L   !    !  +--1cit_A    
                               !    !  
  ----DG--KG--RTRG------   L   !    !        +3cbb_A    
                               !    !     +--1 
  ----EC--KG--KGRG--RC--   L   !    !     !  +2ff0_A    
                               !    !     !  
  --------KGVT--RG------   L   +---15     !        +5cbz_E    
                                    !     !      +-3 
  --------KGVT--RG------   L        !  +-11      ! +2c7a_B    
                                    !  !  !    +-6 
  --------KAVA--RA------   L        !  !  !    ! ! +5e69_A    
                                    !  !  !  +-7 +-2 
  ----EC--KG--KGRA--RT--   L        !  !  !  ! !   +5l0m_A    
                                    +-14  +-10 ! 
  --HAEC--KG--RGRG------   L           !     ! +-1a6y_A    
                                       !     !  
  --HC----KGVT--RG------               !     +--3g9m_B    
                                       !  
  ----ET--KGAT--RG------   L           !  +1lat_A    
                                       +--4 
  --------KGVT--RG------                  +5emc_A    
                             


> 2hdc_A:STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX

  
  ----------------NA----RA--HTSTLT--------------------   L                               +-----2a07_K    
                                                                                      +--2 
  --------ST--------NAST--RTHTST----------------------   L                         +--3  +-----3l2c_A    
                                                                                   !  ! 
  KAFA----------------------------------MC------------                          +--4  +--------3aaf_B    
                                                                                !  ! 
  ------------RGRG--YC--------------------------------   L             +--------5  +-----------1cf7_A    
                                                                       !        ! 
  --------------------------YG------------------------                 !        !           +--4lb5_B    
                                                                 +-----6        +-----------1 
  ----SGQG--YCNC--------------------------------------           !     !                    +--2ve9_C    
                                                               +-7     ! 
  ----YC------HGQT--YTPT--------------LG--------------   L     ! !     +-----------------------5x11_A    
                                                             +-8 ! 
  ----------------------------------------RGVGTGITPTRC   L   ! ! +-----------------------------5v9x_A    
                                                           --9 ! 
  ----------PTPG--TTRG------------------HT------------   L   ! +-----------------------------5xxp_A    
                                                             ! 
  ----------DCKGRGNA--RT----KT----KGRA----------------   L   +-----------------------------5ddg_A    
                                                           


> 2hdd_A:ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX



> 2heo_D:GENERAL STRUCTURE-BASED APPROACH TO THE DESIGN OF PROTEIN LIGANDS: APPLICATION TO THE DESIGN OF KV1.2 POTASSIUM CHANNEL BLOCKERS.

  
  ------------------------------------YG------------------                                              +2heo_D    
                                                                                                +-------1 
  ------------------ST--PTTC----QG------RG----------------   L                                  !       +1f5t_A    
                                                                                                !  
  ------------------TT--PTTC--STNT------------------RT----   L                              +--16      +4lln_I    
                                                                                            !   !  +---6 
  ------------------DCSA--TA--TT--------RT----------RA----   L                              !   !  !   +1z9c_A    
                                                                                            !   +-11  
  ------------SGQG----YCNC--------------------------------                                  !      !     +2ve9_C    
                                                                                            !      !   +-4 
  ------------------LTRTPTNA--VT--------------------RT----   L                           +-19      +---8 +6c2s_D    
                                                                                         !  !          ! 
  --------------------RGSTRT--STHG------------------RA----   L                           !  !          +3zpl_B    
                                                                                         !  !  
  ------------------STQASGAT--STQT------------------QA----   L                           !  !     +------4on0_B    
                                                                                         !  !  +-15  
  ------------------STKTPTTT--FT------------------RA------   L                        +-20  !  !  +------4aso_F    
                                                                                      !  !  +-17  
  ------------------------------------YG------------------                            !  !     !        +4lb5_B    
                                                                                      !  !     +--------5 
  ------------------STPTATAT--TTKG------------------------   L                        !  !              +5yi2_J    
                                                                                      !  !  
  ------------------------------NA----HT--STLT------------   L                        !  !        +-----2a07_K    
                                                                                      !  +-------14  
  ----------TT----------KATT--QTTG----LTRT----KA----FTYT--   L                        !           +-----2p7c_B    
                                                                                   +-22  
  ----------------------RGRG--YC--------------------------   L                     !  !             +----1cf7_A    
                                                                                   !  !       +----10  
  ----------------------HT----RTITYT----------------------   L                     !  !       !     +----4kfc_B    
                                                                                   !  !       !  
  ------------------------------------YGRG----------------                         !  !  +---18          +4wcg_B    
                                                                                   !  !  !    !     +----3 
  --LAHAKARA--------------------------------------------IA                      +-23  !  !    !     !    +6dta_A    
                                                                                !  !  !  !    +----13  
  ------------------------------------YG------------------                      !  !  +-21          !    +4ka4_B    
                                                                                !  !     !          +----2 
  ----------------------KGTA----TA------RG----------------   L                  !  !     !               +1xsd_A    
                                                                             +-24  !     !  
  ------------------QTPTPG--TTRG--------------------HT----   L               !  !  !     +---------------5xxp_A    
                                                                             !  !  !  
  ----------ST------STQAQGST--SART------------------KT----   L               !  !  +-----------------5trd_B    
                                                                          +-25  !  
  ----------------RT--------------------------------------   L            !  !  +--------------------5fmf_V    
                                                                          !  !  
  ------------RG----STRGMCTT--RT--------------------------   L            !  !                     +4u0y_B    
                                                                          !  !                 +---7 
  ------------------TTLTECTA--STRG------------------------   L         +-26  +----------------12   +4i2o_B    
                                                                       !  !                    !  
  ------------------ITRGECSC--SGKG------------------------   L         !  !                    +----5i2d_R    
                                                                       !  !  
  --------------------RG----DTVT----ST----------RC--------   L      +-27  !                     +-4nhj_A    
                                                                    !  !  +---------------------9 
  ----------------------NTVC--ECSTYT--STYC------RA--------   L      !  !                        +-5ed4_A    
                                                                 +-28  !  
  ------------------------------------------------ITHG----   L   !  !  +-------------------------5iyc_T    
                                                               -29  !  
  --------------------MGSGTT--TTYC------------------------   L   !  +---------------------------5f7q_C    
                                                                 !  
  TT------------------------------------------------------   L   +---------------------------3gpl_A    
                                                               


> 2hos_A:PHAGE-SELECTED HOMEODOMAIN BOUND TO UNMODIFIED DNA



> 2i0q_A:CRYSTAL STRUCTURE OF A TELOMERE SINGLE-STRAND DNA-PROTEIN COMPLEX FROM O. NOVA WITH FULL-LENGTH ALPHA AND BETA TELOMERE PROTEINS

  
  ----DGTGFG--YGKT------YT----KG--------------------FGIGHG--RG--YG----QG------------DGDGDGYGTG--LGLGKGPGRGRGSG------------STHTYT--   L          +---------------------2i0q_A    
                                                                                                                                                ! 
  --KGFG----------STTTDT--------------TG--LA--FA------------QG--YG------QGIA--------YT--------------------------------------------   L        +-5    +-----------------3kjp_A    
                                                                                                                                              ! ! +--2 
  ----------------ST--DT--------------QC--HC--FA----------TGRG--YC--RCQCLG--SGKGDG------------------------------------------------            ! +-4  +-----------------6bwy_A    
                                                                                                                                         +----6   ! 
  ------------------------------------------------------------------------------------------KTTT----------------KT----FTSTFTST----   L   !    !   +--------------------4gnx_Z    
                                                                                                                                         !    ! 
  ------------------------YTFT----------NT--SG--WG----------KG--FG------EGKG--KG--TG----------------------------------------------       !    !   +-------------------3u58_C    
                                                                                                                                       --7    +---3 
  ----------------------------------------------------------------------------------QT--------RT----------LT--TT--KTFTQT--------HT       !        !   +---------------4gnx_B    
                                                                                                                                         !        +---1 
  ----------KG----YT--------------------RT--IG--WGDG----------DTHTLTYA------------------------------------------------------------   L   !            +---------------4hja_A    
                                                                                                                                         ! 
  NT--DT----------------------STATNTTTWT------------------------------------------------------------------------------------------       +----------------------------5odn_B    
                                                                                                                                       


> 2i13_A:AART, A SIX FINGER ZINC FINGER DESIGNED TO RECOGNIZE ANN TRIPLETS

  
  RGDCHG--------KGDCRG--QARGATNA----QA--ATHG----RG--DCNA----TT--RGRTDAAT----   L                                +2i13_A    
                                                                                            +-------------------1 
  CTSTQTLTITST--STHTRG--RG----EARA----TTTGEC--RGRG----ET--------RG--SCEC--RG   L         +-14                   +5v3j_F    
                                                                                         !  !  
  ------------------KT--EC--SCKGRG--LT--FCNA----QA--TTNA--------------------   L         !  +-------------------1ubd_C    
                                                                                         !  
  ----------NG--SGHGRG--DA--SCHGRGRGDC--SCNA----NCKTSAHG----RG--------------   L         !                        +5ei9_F    
                                                                                         !                      +-2 
  ----------------------KT--STHT----RG--DAQA--RGRGSTDCHG----TT--RG--DAEG--RG   L         !        +-------------6 +6b0o_A    
                                                                                         !        !             ! 
  ----------EC--SCKGRG----TCYCKARG--QA----TC----RA--SCDC----VT--------------   L         !        !             +-5yeg_A    
                                                                                         !        !  
  ----------------------QA--TTNA--STQAQTATSTNTATTTLAHGTC----RG--------------   L   +----15        !               +1g2f_F    
                                                                                   !     !     +-11       +-------4 
  KGWTKA--------HCHGRG--TA--ACNAKG------------------------------------------   L   !     !     !  !       !       +1tf6_A    
                                                                                   !     !     !  !   +---7 
  ----------------------RGSTDTEGRG--RGSGDCHG--TTRG--DAEG----RG--------------   L   !     !     !  !   !   !      +4x9j_A    
                                                                                   !     !     !  !   !   +------5 
  ----------RGSTDAHARG--RGSTDCHGTT--RG--DAEG--RG----------------------------   L   !     !  +-12  +---8          +5kl3_A    
                                                                                   !     !  !  !      ! 
  ----------------------QA--SGNAKG--QASTSCDC--KGRG--DCHA----RG--------------   L   !     !  !  !      !           +1mey_C    
                                                                                 -16     !  !  !      +-----------3 
  --------------TTSGRG------ECYC----NTYGQGFT--------------------------------   L   !     +-13  !                  +5vmy_A    
                                                                                   !        !  !  
  ----------------------QA--TCNA----QAHTTT----QATTLAHGTC--DTRG--------------   L   !        !  +---------------1g2d_F    
                                                                                   !        !  
  --------------------FARGSGSCTCTAHCQA--STDC--KTQASGSANA--IGTT--------------   L   !        !     +-----------2kmk_A    
                                                                                   !        +----10  
  ----------------------RG--DGECRG--RGSGDCHA--------------------------------   L   !              +-----------2wbs_A    
                                                                                   !  
  ----------------------AT--YC------RA----NC------ATSGDC----KG--DCPTSGSARTKG   L   !             +-----------2gli_A    
                                                                                   +-------------9 
  ----------------------------------QG--RGHT--MGQG----LGLC----TTRG----------   L                 +-----------5yel_A    
                                                                                 


> 2i9t_A:STRUCTURE OF NF-KB P65-P50 HETERODIMER BOUND TO PRDII ELEMENT OF B- INTERFERON PROMOTER

  
  RGRGYTCTEC--SG----RT------   L        +2i9t_A    
                                      +-2 
  RGRG----EC--------RGPTKT--   L      ! ! +2ram_A    
                                   +--3 +-1 
  RGRGYTCTEC--------RT------   L   !  !   +1gji_A    
                                   !  ! 
  RGRGYTCTECRG------KT------   L --5  +3do7_A    
                                   ! 
  RGRGYTCCEC----HTKTKTPTKTRG   L   ! +--1nfk_A    
                                   +-4 
  RGRGYTCCEC----HG--KG------   L     +--1a3q_A    
                                 


> 2ih2_D:CRYSTAL STRUCTURE OF THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI COMPLEXED WITH THE COFACTOR ANALOG AETA AND A 10 BP DNA CONTAINING 5- METHYLPYRIMIDIN-2(1H)-ONE AT THE TARGET BASE PARTNER POSITION

  
  NAYAKCYG--KT----FAKAKGVA--FTRGSGPGETRGRTHCTCRCEC--PTHG   L                +--------------2ih2_D    
                                                                  +---------1 
  NAFA----KG----WA--AAACVA------------------------ECRG--   L   +--2         +--------------5hr4_C    
                                                               !  ! 
  ------NG----------------------------------------------   L --3  +------------------------5yx2_D    
                                                               ! 
  DAYA--------TC----------EA----------------------------   L   +---------------------------4zcf_B    
                                                             


> 2iie_A:SINGLE CHAIN INTEGRATION HOST FACTOR PROTEIN (SCIHF2) IN COMPLEX WITH DNA

  
  --------------------------RCRTNAPTKTICRTRARANAPAKT   L                +-------------2iie_A    
                                                           +------------3 
  ------------------------RTRARANAPAKT--------------   L   !            !             +1owf_B    
                                                           !            +-------------1 
  --------------------------RGRT--PTKTIG------------   L   !                          +1p71_B    
                                                         --6 
  ------------NT----NAIARG--------------------------   L   !                     +----1puf_B    
                                                           !        +------------2 
  ------------NC--ITNARGRG--------------------------   L   !   +----4            +----6fqq_E    
                                                           !   !    ! 
  ----RC--RT--NC--ICNARGRG--------------------------   L   +---5    +-----------------6fqp_B    
                                                               ! 
  LTNGRGTG--LCLCRG----------------------------------           +----------------------4ofa_A    
                                                         


> 2irf_L:CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.

  
  --KG----ATNT--RTCT------SC   L                            +-2irf_L    
                                                          +-2 
  HC--------NT--RGCT----NGST   L          +---------------3 +-1if1_B    
                                          !               ! 
  ------------------------RG              !               +--4hly_B    
                                          ! 
  ----KT--RGAT----RGYA------   L   +------6               +--1bc8_C    
                                   !      !        +------4 
  --DCKT--RG------RGYA------   L   !      !        !      ! +1dux_F    
                                   !      +--------5      +-1 
  ----KT--RGSA----RGQA------   L --7               !        +1yo5_C    
                                   !               ! 
  ------ST----RTQT----MT----   L   !               +---------5d8k_B    
                                   ! 
  --------NAST--RTHT----ST--   L   +-------------------------3l2c_A    
                                 


> 2is6_B:CRYSTAL STRUCTURE OF UVRD-DNA-ADPMGF3 TERNARY COMPLEX

  
  FT--HT------------ST--FT------WGRTRT------------HGSTMT----RTEGEGYG                               +-2is6_B    
                                                                                                +--1 
  ----HT----------------FT------FTRTRT--NTAT----RGHTST----ET----ETFT                       +----3  +-4c2u_D    
                                                                                           !    ! 
  FTTTHT----------------FT--DTYTWTRTRT------KTYT--------------------   L   +---------------4    +----2pjr_A    
                                                                           !               ! 
  ----HTDTKTRTATFTLTDTQTFT------WTRTRT------------HTHTSTST----------   L --6               +---------1uaa_B    
                                                                           ! 
  ------------------------HT----VT----------------HT----------------   L   !  +----------------------3gpl_A    
                                                                           +--5 
  ------------------------------------HT----------HT----------------   L      !                  +---5fhd_A    
                                                                              +------------------2 
  ------------------------------------------------------RG----------   L                         +---5o6b_B    
                                                                         


> 2isz_B:CRYSTAL STRUCTURE OF A TWO-DOMAIN IDER-DNA COMPLEX CRYSTAL FORM I

  
  ----------------ST--PTTC--QG----RG------------   L                 +------------1f5t_A    
                                                                 +--16  
  ----------TT--------KATTQTTG--LTRTKA------FTYT   L             !   !        +---2p7c_B    
                                                                 !   +--------8 
  ----------------STPTATATTTKG------------------   L             !            +---5yi2_J    
                                                                 !  
  ----------------TT--PTTCSTNT------------------   L             !                    +4lln_I    
                                                                 !                  +-6 
  ----------------DCSA--TATT------RT------------   L             !              +---7 +1z9c_A    
                                                                 !              !   ! 
  ------------------RGTCTA--RGNT------RT--------   L          +-18           +-11   +-4fx4_B    
                                                              !  !           !  !  
  ------------------RGSTRTSTHG--------RA--------   L          !  !  +-------12  +-----3zpl_B    
                                                              !  !  !        !  
  --------------------QC------------------------              !  !  !        +-------5hso_A    
                                                              !  !  !  
  ------------------------------YG--------------              !  !  !                 +2heo_D    
                                                              !  !  !               +-1 
  ------------------------------YGRG------------              !  +-17               ! +4wcg_B    
                                                              !     !           +---5 
  ------------------------------YG--------------              !     !           !   ! +4ka4_B    
                                                              !     !       +--10   +-3 
  --------------------KGTA--TA----RG------------   L      +--19     !       !   !     +1xsd_A    
                                                          !   !     !       !   !  
  ------------RG--STRGMCTTRT--------------------   L      !   !     !       !   +----4u0y_B    
                                                          !   !     +------13  
  ------------SGQG--YCNC------------------------          !   !             !        +2ve9_C    
                                                          !   !             !   +----2 
  ----------------LTRTPTNAVT--------------------   L      !   !             +---9    +6c2s_D    
                                                          !   !                 ! 
  ----------------STQASGATSTQT------------QA----   L   +-20   !                 +----4on0_B    
                                                       !  !   !  
  RC------------------RGRGYC--------------------   L   !  !   !                   +1cf7_A    
                                                       !  !   !         +---------4 
  --TTQT----------------------------------------   L   !  !   +--------14         +3gpl_A    
                                                       !  !             !  
  ----------------STKTPTTTFT--------------------   L -21  !             +---------4aso_F    
                                                       !  !  
  ----------------STQTPTPGTTRG----------HT------   L   !  !            +----------5xxp_A    
                                                       !  +-----------15  
  ----------ST----STQAQGSTSART------------------   L   !               +----------5trd_B    
                                                       !  
  ------KAFA--------------------------FGMC------       +-------------------------3aaf_B    
                                                     


> 2itl_B:THE ORIGIN BINDING DOMAIN OF THE SV40 LARGE T ANTIGEN BOUND TO THE FUNCTIONAL PEN PALINDROME DNA (23 BP)

  
  ----SANGKGTC------------RG--------------   L                       +-----------3qfq_B    
                                                      +--------------1 
  --NT--KTTTTC----------------------------            !              +-----------1ksy_A    
                                                   +--3 
  ----------------RT--RTYT------VTQT------         !  !      +-------------------1uut_A    
                                                 +-4  +------2 
  YG------------------------RTKC----AG----   L   ! !         +-------------------4er8_A    
                                               --5 ! 
  ------------KTTGYCNG--RT----------------   L   ! +-----------------------------1b3t_A    
                                                 ! 
  ------------------------------------YCAG       +-----------------------------2bcq_A    
                                               


> 2kdz_A:STRUCTURE OF THE R2R3 DNA BINDING DOMAIN OF MYB1 PROTEIN FROM PROTOZOAN PARASITE TRICHOMONAS VAGINALIS IN COMPLEX WITH MRE-1/MRE-2R DNA

  
  NA--RTQT--EC------------NG--NA------   L                              +2kdz_A    
                                                                     +--1 
  ----KG--RAEA----------DCNAKGNANTST--   L       +-------------------5  +3zqc_A    
                                                 !                   ! 
  ----KG--RTEC------------NAKGNANTST--   L       !                   +---1h89_C    
                                             +---6 
  ----------------RA----RCET--SAQAKG--   L   !   !                     +-5lxu_A    
                                             !   !                   +-2 
  ----------------RT----------VAQTNA--   L   !   !                   ! +-5hod_A    
                                           --7   +-------------------4 
  ----------------------------ITQTNARG   L   !                       ! +-6dfy_D    
                                             !                       +-3 
  --STVC--KGDCRG----------------------   L   !                         +-1w0t_A    
                                             ! 
  --------------RT--HGSGRGHGRT--------   L   +---------------------------1tc3_C    
                                           


> 2kmk_A:GFI-1 ZINC FINGERS 3-5 COMPLEXED WITH DNA

  
  EC--SCKGRG----TCYCKA--RGQA----TC----   L                 +------5yeg_A    
                                                           ! 
  QARGATNA----QA--ATHG----RG--DCNATT--   L     +-----------5       +2i13_A    
                                               !           ! +-----2 
  --TTTGECRG--RG----ET----RG--SCECRG--   L     !           ! !     +5v3j_F    
                                               !           +-4 
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L   +-7             !     +1g2f_F    
                                             ! !             +-----1 
  RG--DAQARG--RGSTDCHG--TTRG--DAEGRG--   L   ! !                   +6b0o_A    
                                             ! ! 
  ----TTSGRG------ECYC----NTYGQGFT----   L --8 +------------------5vmy_A    
                                             ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L   !                  +5kl3_A    
                                             ! +----------------3 
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L   +-6                +1tf6_A    
                                               ! 
  ------------RG--DGEC--RGRGSGDCHA----   L     +----------------2wbs_A    
                                           


> 2ky8_A:SOLUTION STRUCTURE AND DYNAMIC ANALYSIS OF CHICKEN MBD2 METHYL BINDING DOMAIN BOUND TO A TARGET METHYLATED DNA SEQUENCE

  
  RG--KC----RG   L                     +-2ky8_A    
                                +------2 
  RG--------RG                  !      +-6ccg_B    
                     +----------3 
  RGTTRT--YARG       !          !        +6d1t_A    
                   --4          +--------1 
  RG----DC--RG       !                   +6c1t_D    
                     ! 
  RG------YCRG       +-------------------6c1y_A    
                   


> 2ld5_A:SOLUTION NMR-DERIVED COMPLEX STRUCTURE OF HOXA13 DNA BINDING DOMAIN BOUND TO DNA



> 2lef_A:LEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 STRUCTURES

  
  KC--NT--MAMA--EGSAACNT----YTKCRTKT   L      +----2lef_A    
                                              ! 
  RT--NTFTMA--RT--NG--SA--YA--------   L   +--3   +-4y60_C    
                                           !  ! +-1 
  RC--NTFTMA--RAHGNT--SA--YA--------   L   !  +-2 +-3f27_D    
                                         --4    ! 
  ----STYGLASGLA--TGTCIT------------   L   !    +--3tq6_B    
                                           ! 
  RTTASTYAFALT----PTATSTRA----------   L   +-------5jh0_D    
                                         


> 2lkx_A:NMR STRUCTURE OF THE HOMEODOMAIN OF PITX2 IN COMPLEX WITH A TAATCC DNA BINDING SITE



> 2me6_A:NMR STRUCTURE OF THE HOMEODOMAIN TRANSCRIPTION FACTOR GBX1 FROM HOMO SAPIENS IN COMPLEX WITH THE DNA SEQUENCE CGACTAATTAGTCG



> 2n8a_A:1H, 13C AND 15N CHEMICAL SHIFT ASSIGNMENTS AND SOLUTION STRUCTURE FOR PARP-1 F1F2 DOMAINS IN COMPLEX WITH A DNA SINGLE-STRAND BREAK

  
  --RGSTFGVTPCRG--QCLCIG   L               +------------2n8a_A    
                                  +--------1 
  ------------RGKG--LCIG       +--2        +------------3odc_B    
                               !  ! 
  --RG--FCVGPG----------     --3  +---------------------3od8_G    
                               ! 
  STRG------------------       +------------------------4av1_A    
                             


> 2nll_B:RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA

  
  ----EC--KG--RGRG------KA   L       +-----2nll_B    
                                     !  
  ----EA--KG--RTRG--------   L   +--15     +1kb2_B    
                                 !   !   +-7 
  ----EA--KG--RTRTRT------       !   +---9 +2han_B    
                                 !       ! 
  ----EC--KA--RGRG--------   L   !       +-4nqa_I    
                                 !  
  CA--EC--KG--KGRG------RT   L -16    +----1cit_A    
                                 !    !  
  ----EC--KG--KGRG--------   L   !    !     +--1dsz_B    
                                 !    !  +-11  
  ----DG--KG--RTRG--------   L   !    !  !  !  +3cbb_A    
                                 !    !  !  +--1 
  --HGECAGKGAAKGRT--------   L   +---14  !     +1lo1_A    
                                      !  !  
  --------KGVT--RG--------   L        !  !         +2c7a_B    
                                      !  !       +-6 
  --------KAVA--RA--------   L        !  !       ! ! +5e69_A    
                                      !  !       ! +-2 
  --------KGVT--RG--------   L        +-13       !   +5cbz_E    
                                         !     +-8 
  ----ET--KGAT--RG--------   L           !     ! !     +1lat_A    
                                         !     ! !   +-3 
  ----EC--KG--KGRA--RT----   L           !     ! ! +-4 +5l0m_A    
                                         !  +-10 ! ! ! 
  ----EC--KG--KGRG--------   L           !  !  ! +-5 +2ff0_A    
                                         !  !  !   ! 
  --------KGVT--RG--------               +-12  !   +5emc_A    
                                            !  !  
  --HAEC--KG--RGRG--------   L              !  +-1a6y_A    
                                            !  
  --HC----KGVT--RG----RT--                  +--3g9m_B    
                               


> 2nqb_D:DROSOPHILA NUCLEOSOME STRUCTURE



> 2nqb_G:DROSOPHILA NUCLEOSOME STRUCTURE



> 2o4a_A:CRYSTAL STRUCTURE OF THE N-TERMINAL CUT DOMAIN OF SATB1 BOUND TO MATRIX ATTACHMENT REGION DNA

  
  ----TTQA--LTSAET--------   L                       +-----2o4a_A    
                                           +---------2 
  ----SAQA--TCSADT--------   L             !         +-----2d5v_B    
                                 +---------3 
  --AT--QAAT--SA----------       !         !          +----4z5h_A    
                               --4         +----------1 
  QT--STNTVTATSTQTRTET----   L   !                    +----2r1j_L    
                                 ! 
  ----NTQASAHTSTQT----TTPG   L   +-------------------------1ic8_B    
                               


> 2o8b_B:HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO ADP AND A G T MISPAIR

  
  VCKCFGETMT----PG         +------2o8b_B    
                         +-3 
  --YGKA------SAPA       ! +------3thx_B    
                       --4 
  MGDAFGTT--MC--PT   L   !     +--1wb9_A    
                         !  +--1 
  ----FGET--------       +--2  +--1ewq_A    
                            ! 
  --DGFG------VGSG          +-----3thx_A    
                       


> 2ofi_A:CRYSTAL STRUCTURE OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG) BOUND TO DNA/3MA

  
  AA--LA----ITHT--KT----       +-------------------2ofi_A    
                               ! 
  NGRGTG--------LG--LCRG       !           +--------4ew0_A    
                               !         +-6 
  ------------YG--------   L --8         ! !     +--5kn8_A    
                               !         ! +-----4 
  --QGCGTA----LC--------       !         !       +--1orn_A    
                               !         ! 
  QGKGLGSGAG--SCLTKC----       +---------7         +4b21_A    
                                         !       +-2 
  --QTLAHGAT------KT----                 !       ! +3s6i_A    
                                         !     +-3 
  --NA--RA------FGRC----   L             !     ! ! +3i0w_A    
                                         +-----5 +-1 
  --NG--RG------FGRC----                       !   +4ejy_A    
                                               ! 
  --NCNANARC----YGRC----                       +---2xhi_A    
                             


> 2p5l_D:CRYSTAL STRUCTURE OF A DIMER OF N-TERMINAL DOMAINS OF AHRC IN COMPLEX WITH AN 18BP DNA OPERATOR SITE

  
  --------------------NAHT--LT----------------------   L                               +-----2a07_K    
                                                                                    +-11  
  --TT----------KATG----LTRT--KA--------------FT--YT   L                     +-----12  +-----2p7c_B    
                                                                             !      !  
  --------------------------------------YANAKTFGMC--                         !      +------3aaf_B    
                                                                          +-14  
  ----SGQG------------------------------------------                      !  !           +-2ve9_C    
                                                                          !  !           ! 
  ----------------------YGRG------------------------                      !  +-----------9   +4wcg_B    
                                                                          !              ! +-7 
  ----------------------YG--------------------------          +----------16              +-8 +4lb5_B    
                                                              !           !                ! 
  ----------------------YG--------------------------          !           !                +-4ka4_B    
                                                              !           !  
  ----------TA----TA------RG------------------------   L   +-19           !  +--------------1xsd_A    
                                                           !  !           +-15  
  ------------------NASTHT--ST----------------------   L   !  !              +--------------3l2c_A    
                                                           !  !  
  PT------RT----------------------------------------   L   !  !     +--------------------5fmf_V    
                                                           !  +----17  
  ----------------------------------RGKG--------NT--   L   !        +--------------------5vfx_A    
                                                           !  
  ----------------------IT--QTNA--RG----------------   L   !                               +6dfy_D    
                                                           !                             +-1 
  --------------------RTVA--IANAMCRG----------------   L -20                    +--------2 +1le8_A    
                                                           !                    !        ! 
  ----------------------VA--SGNA--------------------   L   !                    !        +3cmy_A    
                                                           !                    !  
  ----------------------VA--QTNA--------------------   L   !                    !         +1fjl_B    
                                                           !     +-------------13       +-4 
  ----------------------VA--QTNA--------------------   L   !     !              !       ! +