2PZS
Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0001882 | molecular_function | nucleoside 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 | 0039693 | biological_process | viral DNA genome replication |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0001882 | molecular_function | nucleoside binding |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| B | 0004527 | molecular_function | exonuclease activity |
| B | 0006260 | biological_process | DNA replication |
| B | 0039693 | biological_process | viral DNA genome replication |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0001882 | molecular_function | nucleoside binding |
| C | 0003676 | molecular_function | nucleic acid binding |
| C | 0003677 | molecular_function | DNA binding |
| C | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| C | 0004527 | molecular_function | exonuclease activity |
| C | 0006260 | biological_process | DNA replication |
| C | 0039693 | biological_process | viral DNA genome replication |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0001882 | molecular_function | nucleoside binding |
| D | 0003676 | molecular_function | nucleic acid binding |
| D | 0003677 | molecular_function | DNA binding |
| D | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| D | 0004527 | molecular_function | exonuclease activity |
| D | 0006260 | biological_process | DNA replication |
| D | 0039693 | biological_process | viral DNA genome replication |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PROSITE/UniProt
| site_id | PS00116 |
| Number of Residues | 9 |
| Details | DNA_POLYMERASE_B DNA polymerase family B signature. YCDTDSIHL |
| Chain | Residue | Details |
| A | TYR454-LEU462 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0007744|PDB:1XI1 |
| Chain | Residue | Details |
| A | ASP145 | |
| A | ASP169 | |
| B | ASP145 | |
| B | ASP169 | |
| C | ASP145 | |
| C | ASP169 | |
| D | ASP145 | |
| D | ASP169 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:8226957, ECO:0007744|PDB:2PYJ |
| Chain | Residue | Details |
| A | ASP249 | |
| B | ASP249 | |
| C | ASP249 | |
| D | ASP249 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19883660, ECO:0007744|PDB:2PYJ |
| Chain | Residue | Details |
| A | VAL250 | |
| B | VAL250 | |
| C | VAL250 | |
| D | VAL250 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0007744|PDB:2PYL |
| Chain | Residue | Details |
| B | TYR254 | |
| B | LYS371 | |
| B | LYS383 | |
| B | ASP458 | |
| C | TYR254 | |
| C | LYS371 | |
| C | LYS383 | |
| C | ASP458 | |
| D | TYR254 | |
| D | LYS371 | |
| D | LYS383 | |
| D | ASP458 | |
| A | TYR254 | |
| A | LYS371 | |
| A | LYS383 | |
| A | ASP458 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:9784372 |
| Chain | Residue | Details |
| A | ASP456 | |
| B | ASP456 | |
| C | ASP456 | |
| D | ASP456 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | SITE: Essential for 3'-5' exonucleolysis => ECO:0000269|PubMed:2790959, ECO:0000269|PubMed:8344956 |
| Chain | Residue | Details |
| B | GLU14 | |
| B | ALA66 | |
| C | ALA12 | |
| C | GLU14 | |
| C | ALA66 | |
| D | ALA12 | |
| D | GLU14 | |
| D | ALA66 | |
| A | ALA12 | |
| A | GLU14 | |
| A | ALA66 | |
| B | ALA12 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | SITE: Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site => ECO:0000269|PubMed:8605889 |
| Chain | Residue | Details |
| A | THR15 | |
| A | ASN62 | |
| B | THR15 | |
| B | ASN62 | |
| C | THR15 | |
| C | ASN62 | |
| D | THR15 | |
| D | ASN62 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 12 |
| Details | SITE: Interaction with the primer terminal protein => ECO:0000269|PubMed:11884636 |
| Chain | Residue | Details |
| A | TYR59 | |
| A | HIS61 | |
| A | PHE69 | |
| B | TYR59 | |
| B | HIS61 | |
| B | PHE69 | |
| C | TYR59 | |
| C | HIS61 | |
| C | PHE69 | |
| D | TYR59 | |
| D | HIS61 | |
| D | PHE69 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 12 |
| Details | SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269|PubMed:9786901 |
| Chain | Residue | Details |
| C | LEU123 | |
| D | PHE65 | |
| D | SER122 | |
| D | LEU123 | |
| A | PHE65 | |
| A | SER122 | |
| A | LEU123 | |
| B | PHE65 | |
| B | SER122 | |
| B | LEU123 | |
| C | PHE65 | |
| C | SER122 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | SITE: Involved in binding template-primer structures => ECO:0000269|PubMed:8344956 |
| Chain | Residue | Details |
| A | ILE93 | |
| B | ILE93 | |
| C | ILE93 | |
| D | ILE93 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | SITE: Involved in the stabilization of the frayed 3' terminus at the exonuclease active site => ECO:0000269|PubMed:19576228 |
| Chain | Residue | Details |
| A | TYR148 | |
| B | TYR148 | |
| C | TYR148 | |
| D | TYR148 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | SITE: Probably involved in binding template-primer structures => ECO:0000269|PubMed:8226957 |
| Chain | Residue | Details |
| A | SER252 | |
| B | SER252 | |
| C | SER252 | |
| D | SER252 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 8 |
| Details | SITE: Probably involved in nucleotide binding selection => ECO:0000269|PubMed:8537389 |
| Chain | Residue | Details |
| C | TYR254 | |
| C | TYR390 | |
| D | TYR254 | |
| D | TYR390 | |
| A | TYR254 | |
| A | TYR390 | |
| B | TYR254 | |
| B | TYR390 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 8 |
| Details | SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269|PubMed:8605889 |
| Chain | Residue | Details |
| C | THR356 | |
| C | GLU420 | |
| D | THR356 | |
| D | GLU420 | |
| A | THR356 | |
| A | GLU420 | |
| B | THR356 | |
| B | GLU420 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | SITE: Involved in the binding of DNA and dNTP => ECO:0000269|PubMed:11917008 |
| Chain | Residue | Details |
| A | ILE364 | |
| B | ILE364 | |
| C | ILE364 | |
| D | ILE364 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 8 |
| Details | SITE: Stabilization of the incoming nucleotide => ECO:0000269|PubMed:14672657 |
| Chain | Residue | Details |
| A | LYS366 | |
| A | LYS379 | |
| B | LYS366 | |
| B | LYS379 | |
| C | LYS366 | |
| C | LYS379 | |
| D | LYS366 | |
| D | LYS379 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | SITE: Interacts with the phosphate groups of the incoming nucleotide => ECO:0000269|PubMed:11917008 |
| Chain | Residue | Details |
| A | LYS371 | |
| B | LYS371 | |
| C | LYS371 | |
| D | LYS371 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | SITE: Probably involved in nucleotide binding selection => ECO:0000269|PubMed:9199402 |
| Chain | Residue | Details |
| A | LYS383 | |
| B | LYS383 | |
| C | LYS383 | |
| D | LYS383 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | SITE: Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity => ECO:0000269|PubMed:12805385 |
| Chain | Residue | Details |
| A | LEU384 | |
| B | LEU384 | |
| C | LEU384 | |
| D | LEU384 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 8 |
| Details | SITE: Probably involved in binding template-primer structures => ECO:0000269|PubMed:8344956 |
| Chain | Residue | Details |
| C | ASN387 | |
| C | GLY391 | |
| D | ASN387 | |
| D | GLY391 | |
| A | ASN387 | |
| A | GLY391 | |
| B | ASN387 | |
| B | GLY391 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 8 |
| Details | SITE: Probably involved in binding template-primer structures => ECO:0000269|PubMed:7962004 |
| Chain | Residue | Details |
| C | THR434 | |
| C | ARG438 | |
| D | THR434 | |
| D | ARG438 | |
| A | THR434 | |
| A | ARG438 | |
| B | THR434 | |
| B | ARG438 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 8 |
| Details | SITE: Probably involved in binding template-primer structures => ECO:0000269|PubMed:7852344 |
| Chain | Residue | Details |
| A | LYS498 | |
| A | TYR500 | |
| B | LYS498 | |
| B | TYR500 | |
| C | LYS498 | |
| C | TYR500 | |
| D | LYS498 | |
| D | TYR500 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 4 |
| Details | SITE: Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities => ECO:0000269|PubMed:24023769 |
| Chain | Residue | Details |
| A | LYS529 | |
| B | LYS529 | |
| C | LYS529 | |
| D | LYS529 |
