3SQ0
DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+)
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 | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
A | 0004527 | molecular_function | exonuclease activity |
A | 0006260 | biological_process | DNA replication |
A | 0006261 | biological_process | DNA-templated DNA replication |
A | 0008408 | molecular_function | 3'-5' exonuclease activity |
A | 0039686 | biological_process | bidirectional double-stranded viral DNA replication |
A | 0039693 | biological_process | viral DNA genome replication |
A | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE DUP A 904 |
Chain | Residue |
A | ASP411 |
A | THR622 |
A | ASP623 |
A | MN905 |
A | MN906 |
A | HOH922 |
A | HOH923 |
A | HOH978 |
A | HOH1062 |
A | HOH1073 |
P | DOC115 |
A | LEU412 |
T | DA4 |
T | DG5 |
A | THR413 |
A | SER414 |
A | LEU415 |
A | TYR416 |
A | ARG482 |
A | LYS560 |
A | ASN564 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN A 905 |
Chain | Residue |
A | ASP411 |
A | LEU412 |
A | ASP623 |
A | DUP904 |
A | MN906 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN A 906 |
Chain | Residue |
A | ASP411 |
A | ASP623 |
A | DUP904 |
A | MN905 |
A | HOH922 |
A | HOH1118 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN A 907 |
Chain | Residue |
A | GLU686 |
A | GLU716 |
A | HOH978 |
A | HOH1070 |
A | HOH1073 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN A 908 |
Chain | Residue |
A | ASP114 |
A | GLU116 |
A | HOH934 |
A | HOH1139 |
site_id | AC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MN A 909 |
Chain | Residue |
A | HOH946 |
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 | 2 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100 |
Chain | Residue | Details |
A | ASP114 | |
A | GLU116 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497 |
Chain | Residue | Details |
A | ALA222 | |
A | ALA327 |
Chain | Residue | Details |
A | ASP411 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
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 |
Chain | Residue | Details |
A | SER414 | |
A | ARG482 |
Chain | Residue | Details |
A | LYS560 |
Chain | Residue | Details |
A | ASP623 |
site_id | SWS_FT_FI8 |
Number of Residues | 1 |
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 |
site_id | SWS_FT_FI9 |
Number of Residues | 1 |
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 |
site_id | SWS_FT_FI10 |
Number of Residues | 1 |
Details | SITE: Essential for viral replication => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:24116139 |
Chain | Residue | Details |
A | ASP714 |