4I9Q
Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000166 | molecular_function | nucleotide binding |
A | 0003676 | molecular_function | nucleic acid binding |
A | 0003677 | molecular_function | DNA binding |
A | 0003824 | molecular_function | catalytic activity |
A | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
A | 0004518 | molecular_function | nuclease activity |
A | 0004527 | molecular_function | exonuclease activity |
A | 0006260 | biological_process | DNA replication |
A | 0006287 | biological_process | base-excision repair, gap-filling |
A | 0006297 | biological_process | nucleotide-excision repair, DNA gap filling |
A | 0008152 | biological_process | metabolic process |
A | 0008296 | molecular_function | 3'-5'-DNA exonuclease activity |
A | 0008408 | molecular_function | 3'-5' exonuclease activity |
A | 0009432 | biological_process | SOS response |
A | 0016740 | molecular_function | transferase activity |
A | 0016779 | molecular_function | nucleotidyltransferase activity |
A | 0016787 | molecular_function | hydrolase activity |
A | 0039686 | biological_process | bidirectional double-stranded viral DNA replication |
A | 0039693 | biological_process | viral DNA genome replication |
A | 0045004 | biological_process | DNA replication proofreading |
A | 0046872 | molecular_function | metal ion binding |
B | 0000166 | molecular_function | nucleotide binding |
B | 0003676 | molecular_function | nucleic acid binding |
B | 0003677 | molecular_function | DNA binding |
B | 0003824 | molecular_function | catalytic activity |
B | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
B | 0004518 | molecular_function | nuclease activity |
B | 0004527 | molecular_function | exonuclease activity |
B | 0006260 | biological_process | DNA replication |
B | 0006287 | biological_process | base-excision repair, gap-filling |
B | 0006297 | biological_process | nucleotide-excision repair, DNA gap filling |
B | 0008152 | biological_process | metabolic process |
B | 0008296 | molecular_function | 3'-5'-DNA exonuclease activity |
B | 0008408 | molecular_function | 3'-5' exonuclease activity |
B | 0009432 | biological_process | SOS response |
B | 0016740 | molecular_function | transferase activity |
B | 0016779 | molecular_function | nucleotidyltransferase activity |
B | 0016787 | molecular_function | hydrolase activity |
B | 0039686 | biological_process | bidirectional double-stranded viral DNA replication |
B | 0039693 | biological_process | viral DNA genome replication |
B | 0045004 | biological_process | DNA replication proofreading |
B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE XG4 A 1001 |
Chain | Residue |
A | LEU412 |
A | CA1003 |
A | NA1004 |
A | HOH1105 |
A | HOH1314 |
A | HOH1316 |
P | DC115 |
T | DC4 |
T | DG5 |
A | SER414 |
A | LEU415 |
A | TYR416 |
A | ARG482 |
A | LYS560 |
A | ASN564 |
A | THR622 |
A | ASP623 |
site_id | AC2 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE XG4 A 1002 |
Chain | Residue |
A | SER36 |
A | PHE38 |
A | LYS48 |
A | TYR49 |
A | ARG59 |
A | MET85 |
A | PHE370 |
A | LYS374 |
A | ASN377 |
A | LYS378 |
A | VAL379 |
A | ILE380 |
A | HOH1218 |
site_id | AC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CA A 1003 |
Chain | Residue |
A | ASP411 |
A | LEU412 |
A | XG41001 |
A | HOH1315 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE NA A 1004 |
Chain | Residue |
A | LEU412 |
A | THR413 |
A | SER414 |
A | LEU415 |
A | ASP623 |
A | XG41001 |
site_id | AC5 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE XG4 B 1001 |
Chain | Residue |
B | LEU412 |
B | SER414 |
B | LEU415 |
B | TYR416 |
B | ARG482 |
B | LYS560 |
B | ASN564 |
B | ASP623 |
B | CA1003 |
B | NA1004 |
B | HOH1120 |
B | HOH1233 |
B | HOH1234 |
C | DC115 |
D | DC4 |
D | DG5 |
site_id | AC6 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE XG4 B 1002 |
Chain | Residue |
B | TYR33 |
B | SER36 |
B | PHE38 |
B | LYS48 |
B | TYR49 |
B | ARG59 |
B | GLY84 |
B | MET85 |
B | ASP95 |
B | PHE370 |
B | LYS374 |
B | ASN377 |
B | LYS378 |
B | ILE380 |
B | HOH1195 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA B 1003 |
Chain | Residue |
B | ASP411 |
B | LEU412 |
B | XG41001 |
site_id | AC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE NA B 1004 |
Chain | Residue |
B | LEU412 |
B | THR413 |
B | SER414 |
B | LEU415 |
B | ASP623 |
B | XG41001 |
Functional Information from PROSITE/UniProt
site_id | PS00116 |
Number of Residues | 9 |
Details | DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV |
Chain | Residue | Details |
A | TYR619-VAL627 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100 |
Chain | Residue | Details |
A | ASP114 | |
A | GLU116 | |
B | ASP114 | |
B | GLU116 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497 |
Chain | Residue | Details |
A | ALA222 | |
A | ALA327 | |
B | ALA222 | |
B | ALA327 |
Chain | Residue | Details |
A | ASP411 | |
B | ASP411 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY |
Chain | Residue | Details |
A | LEU412 | |
B | LEU412 |
Chain | Residue | Details |
A | SER414 | |
A | ARG482 | |
B | SER414 | |
B | ARG482 |
Chain | Residue | Details |
A | LYS560 | |
B | LYS560 |
Chain | Residue | Details |
A | ASP623 | |
B | ASP623 |
site_id | SWS_FT_FI8 |
Number of Residues | 2 |
Details | SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:20166752, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:24116139 |
Chain | Residue | Details |
A | ASP621 | |
B | ASP621 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:22571765 |
Chain | Residue | Details |
A | LYS706 | |
B | LYS706 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | SITE: Essential for viral replication => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:24116139 |
Chain | Residue | Details |
A | ALA714 | |
B | ALA714 |