5D4B
Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| A | 0006281 | biological_process | DNA repair |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0034061 | molecular_function | DNA polymerase activity |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| B | 0006281 | biological_process | DNA repair |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0034061 | molecular_function | DNA polymerase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 601 |
| Chain | Residue |
| A | ASP343 |
| A | ASP345 |
| C | DC6 |
| C | SO4401 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue NA A 602 |
| Chain | Residue |
| A | THR253 |
| A | VAL255 |
| A | VAL258 |
| C | DA4 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 603 |
| Chain | Residue |
| A | MET339 |
| A | THR340 |
| A | LYS338 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 604 |
| Chain | Residue |
| A | LYS469 |
| A | ARG480 |
| B | SER207 |
| B | LYS209 |
| B | GLU467 |
| B | ARG468 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 601 |
| Chain | Residue |
| B | ASP343 |
| B | ASP345 |
| B | SO4603 |
| B | HOH702 |
| D | DC6 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue NA B 602 |
| Chain | Residue |
| B | THR253 |
| B | VAL255 |
| B | VAL258 |
| D | DA4 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 B 603 |
| Chain | Residue |
| B | GLY332 |
| B | GLY333 |
| B | ARG336 |
| B | ASP345 |
| B | MG601 |
| B | HOH702 |
| B | HOH707 |
| D | DC6 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 604 |
| Chain | Residue |
| B | LYS338 |
| B | MET339 |
| B | THR340 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 605 |
| Chain | Residue |
| A | LYS426 |
| B | LYS426 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 606 |
| Chain | Residue |
| B | ASN184 |
| B | GLU185 |
| B | GLY186 |
| B | SER187 |
| E | DA1 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 C 401 |
| Chain | Residue |
| A | GLY332 |
| A | GLY333 |
| A | ARG336 |
| A | LYS338 |
| A | ASP345 |
| A | MG601 |
| C | DC6 |
| C | HOH503 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 402 |
| Chain | Residue |
| C | DA5 |
| C | DC6 |
| C | HOH501 |
| C | HOH502 |
Functional Information from PROSITE/UniProt
| site_id | PS00522 |
| Number of Residues | 20 |
| Details | DNA_POLYMERASE_X DNA polymerase family X signature. GGFrRGkmtGhDVDFLItsP |
| Chain | Residue | Details |
| A | GLY332-PRO351 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | Region: {"description":"Involved in DNA binding","evidences":[{"source":"PubMed","id":"11823435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23856622","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4I2B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I2C","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I2D","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I2E","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 3 |
| Details | M-CSA 632 |
| Chain | Residue | Details |
| A | ASP343 | metal ligand |
| A | ASP345 | metal ligand |
| A | ASP434 | metal ligand, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 3 |
| Details | M-CSA 632 |
| Chain | Residue | Details |
| B | ASP343 | metal ligand |
| B | ASP345 | metal ligand |
| B | ASP434 | metal ligand, proton acceptor, proton donor |
