triangle PDBeMotif: 2oq4  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
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Enzyme   3.2.2.   4.2.99.18
Classification hydrolase/dna    | release date: Wed, Jan 31, 2007
Title crystal structure of the dna repair enzyme endonuclease- viii (nei) from e. coli (e2q) in complex with ap-site containing dna substrate
Authors A.P.GROLLMAN, D.O.ZHARKOV, G.GOLAN, G.SHOAHM
Method X-RAY DIFFRACTION (resolution: 2.60Å)
PDBe Citation   
Small molecules:    search ZN ZN binding statistics ZN   search SO4 SO4 binding statistics SO4   search NA NA binding statistics NA
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,B sequence:
PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTG
EEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQ
AFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC
GSIIEKTTLSSRPFYWCPGCQH
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : ENDONUCLEASE VIII
member of: CATH:search1.10.8.50/search3.20.190.10GENE3D:searchG3DSA_1.10.8.50/searchG3DSA_3.20.190.10HAMAP:searchMF_01253PANTHER:searchPTHR22993PFAM:searchPF01149/searchPF06827/searchPF06831PROSITE PATTERNS:searchPS01242, PROSITE PROFILES:searchPS51066/searchPS51068, SMART:searchSM00898SUPERFAMILY:searchSSF46946/searchSSF57716/searchSSF81624UniProt:searchP50465
JMol viewer RasMol script viewer  SO4 601A  ..*   *                                                                                                                                                                                                              * ..SO4 ..                                       
JMol viewer RasMol script viewer  ZN 501A  ..|   |                                                                                                                                                                                                              | ..ZN ..             *  *                *  *  
sec str:  ...hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhh...eeeeee...eeeeee....eeeee.....eeeeee..........eeeeee...eeeeee...eeeee..hhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh.... .......................eeee....eeee......
sequence :  ..PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRG... ..LFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201          ... ..224       234       244       254      
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..||            | || |      | || || ||| ||||  || |  |||      | |     | |||     || ||  ^**  ||           ||| |       | |||        |  || |       |  ^**|  |    |  | | |  | |  ||     ||||  ||  | | | |    |  ||   | | || ..PS00005..       ||| | |  | |  |    ^**    || || 
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..||            | || |      | || || ||| ||||  ^***  |||      | |     | |||     |^***  | |  ||           |^***       | |||        |  || |       |  |  |  |    |  | | |  | |  ||     ||||  ||  | | | |    |  ||   | | || ..PS00006..       ||| | |  | ^***           || || 
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..||            | || |      | || || ||| ||^*****    |||      | |     | |||     |  |   | |  ||           | |         | |||        |  || |       |  |  |  |    |  | | |  | |  ||     |^*****|  | | | |    |  ||   | | || ..PS00008..       ||| | |  | |              || || 
search RasMol script viewer Motif-ligand binding stats  ZF_FPG_1 ..||            | || |      | || || ||| || |        |||      | |     | |||     |  |   | |  ||           | |         | |||        |  || |       |  |  |  |    |  | | |  | |  ||     | ||  ||  | | | |    |  ||   | | || ..PS01242..       ||| | ^**^****************^**^* 
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..||            | || |      | ***** |***** |        |||      | |     | |||     |  |   | |  ||           | |         *****        |  || |       |  |  |  |    |  | | |  | *****     | ||  ||  | | | |    *****   | | || ..alphabetamotif..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  asxmotif ..||            | || |      | || || ||| || |        |||      | |     | |||     |  |   | |  ||           | |         | |||        |  || |       |  |  |  |    |  | | |  | |  |      | ||  ||  | *****    |  |    | | || ..asxmotif..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  asxturn ..||            | || |      | || || ||| || |        |||      | |     | |||     |  |   | |  ||           | |         | |||        |  || |       |  |  |  |    |  *** |  | |  |      | ||  ||  | ***      |  |    | | || ..asxturn..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  betabulge ..||            | || |      | || || ||| || |        |||      | |     | |||     |  |   | |  **           | |         | |||        |  || |       |  |  |  |    |  |   |  | |  |      | ||  ||  |          |  |    | | || ..betabulge..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  betaturn ..||            | ****      | **************        |||      | |     ****|     ****   | |               | |         ****|        ****| |       |  |  ****    |  |   |  | ****      | ||  |****          ****    | | || ..betaturn..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  gammaturn ..||            | || |      | |       |  |          |||      | |       | |     |  |   | |               ***           | |        |  || |       |  |  |  |    |  |   |  |           | ||  |                      | | || ..gammaturn..       ||| |    | |               |  | 
search RasMol script viewer Motif-ligand binding stats  nest ..||            | || |      | |       |  |          |||      ***       | |     |  |   | |                             | |        |  || |       |  |  |  |    |  |   |  |           ***|  |                      | | || ..nest..       *** |    ***               |  | 
search RasMol script viewer Motif-ligand binding stats  niche ..||            ******      ***       ****          ***                ***     ****   ***                             ***        *******       ****  ****    ****   ****              ****                      | **** ..niche..        ****                      **** 
search RasMol script viewer Motif-ligand binding stats  ststaple ..||                                                 |                                | |                                                                                                                       *****  ..ststaple..                                       
search RasMol script viewer Motif-ligand binding stats  stturn ..||                                                 |                                ***                                                                                                                              ..stturn..                                       
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..**                                                 *                                                                                                                                                                 ..REP00000..                                       

chain C : 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'
sec str:  .............
sequence :  ..GCTTCATCCTG
seq num:  ..402        

chain D : 5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3';
JMol viewer RasMol script viewer  SO4 601A  ..     *      
sec str:  ..............
sequence :  ..CAGGAPGAAGCC
seq num:  ..422         

Assembly 2     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain B : ENDONUCLEASE VIII
member of: CATH:search1.10.8.50/search3.20.190.10GENE3D:searchG3DSA_1.10.8.50/searchG3DSA_3.20.190.10HAMAP:searchMF_01253PANTHER:searchPTHR22993PFAM:searchPF01149/searchPF06827/searchPF06831PROSITE PATTERNS:searchPS01242, PROSITE PROFILES:searchPS51066/searchPS51068, SMART:searchSM00898SUPERFAMILY:searchSSF46946/searchSSF57716/searchSSF81624UniProt:searchP50465
JMol viewer RasMol script viewer  NA 701F  ..                                                                                                                                                                                                                    ..NA ..                                   ..   
JMol viewer RasMol script viewer  NA 702B  ..                                                                                                                                                                                                                    ..NA ..                                   ..   
JMol viewer RasMol script viewer  SO4 603B  ..       *   *                                                                                                                                                                                                        ..SO4 ..                                   ..   
JMol viewer RasMol script viewer  SO4 602B  ..       |   |                                                                    ***                                                                                                                                 ..SO4 ..                                   ..   
JMol viewer RasMol script viewer  ZN 501B  ..       |   |                                                                    |||                                                                                                                                 ..ZN ..              *  *                *..*  
sec str:  ....hhhhhhhhhhhhhhhh...eeeeee......hhhhhhh.....eeeee..eeeee.....eeeee.....eee.............eeeeeee...eeeee...eeeeehhhhhh.hhhhhhh.........hhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh... ..........................................
sequence :  ..PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATR... ..ALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWC..CQH
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201         ... ..223       233       243       253  ..260
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..||      |  |||  || |      | |       | ||||  || |  |||      | |     || ||     || ||  ^**  ||   |  |   |||| |    || ||| |  |  |  |  | |||  |  ||  ^**|  |   || || | |  |           |||   | |  || | |  |  ||  |  || || ..PS00005..    | ||||| | |  | |  |    ^**    |..|| 
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..||      |  |||  || |      | |       | ||||  ^***  |||      | |     || ||     |^***  | |  ||   |  |   ||^***    || ||| |  |  |  |  | |||  |  ||  |  |  |   || || | |  |           |||   | |  || | |  |  ||  |  || || ..PS00006..    | ||||| | |  | ^***           |..|| 
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..||      |  |||  || |      | |       | ||^*****    |||      | |     || ||     |  |   | |  ||   |  |   || | |    || ||| |  |  |  |  | |||  |  ||  |  |  |   || || | |  |           |^***** |  || | |  |  ||  |  || || ..PS00008..    | ||||| | |  | |              |..|| 
search RasMol script viewer Motif-ligand binding stats  ZF_FPG_1 ..||      |  |||  || |      | |       | || |        |||      | |     || ||     |  |   | |  ||   |  |   || | |    || ||| |  |  |  |  | |||  |  ||  |  |  |   || || | |  |           | |     |  || | |  |  ||  |  || || ..PS01242..    | ||||| | ^**^****************^..^* 
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..||      ********** |      | |       | || |        |||      | |     || ||     |  |   | |  ||   |  |   || | |    *****| |  |  |  |  | |||  *****  |  |  |   ***** | |  |           | |     |  || | |  *****  |  ***** ..alphabetamotif..    | ||||| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  asxmotif ..||      |  | |  |  |      | |       | || |        |||      | |     || ||     |  |   | |  ||   |  |   || | |    || ||| |  |  |  |  *****  |  ||  |  |  |   || || | |  |           | |     |  |*****  |  |   |  || |  ..asxmotif..    | ||||| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  asxturn ..||      |  | |  |  |      | |       | || |        |||      | |     || ||     |  |   | |  ||   |  |   || | |    || ||| |  |  |  |  ***|   |  ||  |  |  |   || |*** |  |           | |     |  |***    |  |   |  || |  ..asxturn..    | ||||| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  betabulge ..||      |  | |  |  |      | |       | || |        |||      | |     || ||     |  |   | |  **   |  |   || | |    || ||| |  |  |  |  |  |   |  ||  |  |  |   || ||   |  |           | |     |  |       |  |   |  || |  ..betabulge..    | ||||| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  betaturn ..||      **** ****  |      | |       | ****        |||      | |     ****|     |  |   | |       |  |   || | |    ********  |  |  |  ****   ****|  |  |  |   *****   |  |           | |     |  |       ****   |  ****  ..betaturn..    | ****| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  gammaturn ..||              |  |      | |       |  |          |||      | |      |  |     |  |   | |       |  |   |*** |     |   | |  |  |  |  |  |       |  |  |  |    |  |   |  |           | |     |  |              |   |    ..gammaturn..    |  |||| |    | |               ..   
search RasMol script viewer Motif-ligand binding stats  nest ..||              |  |      | |       |  |          |||      ***      |  |     |  |   | |       |  |   |  | |     |   | |  |  |  |  |  |       |  |  |  |    |  |   |  |           ***     |  |              |   |    ..nest..    |  |*** |    ***               ..   
search RasMol script viewer Motif-ligand binding stats  niche ..||              ****      ***       ****          ***               ****     ****   ***       ****   ******     |   ***  ****  *******       ****  ****    ****   ****                   ****              |   |    ..niche..    *********                      ..   
search RasMol script viewer Motif-ligand binding stats  ststaple ..||                                                 |                                                            *****                                                                                      *****    ..ststaple..                                   ..   
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..**                                                 *                                                                                                                                                                ..REP00000..                                   ..   

chain E : 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'
JMol viewer RasMol script viewer  NA 701F  ..         
sec str:  ...........
sequence :  ..TTCATCCTG
seq num:  ..404      

chain F : 5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3';
JMol viewer RasMol script viewer  NA 701F  ..           
sec str:  .............
sequence :  ..CAGGAPGAAGC
seq num:  ..422        

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