Structure of PDB 6hmf Chain B Binding Site BS02

Receptor Information

>6hmf Chain B (length=442) Species: 272844 (Pyrococcus abyssi GE5)

VVLDKYGYPILYYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPP
KVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGLV
NSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGFY
SKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAF
LKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIPD
IFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIYK
LKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGKPGLPMVELLKMR
HLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGVQLVNS
ATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 6hmf Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hmf Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): D404 N450 H497 H560
• Binding residue (residue number reindexed from 1): D231 N277 H324 H383
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.1: exodeoxyribonuclease I.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006260 DNA replication

External links

• PDB: RCSB:6hmf, PDBe:6hmf, PDBj:6hmf
• PDBsum: 6hmf
• PubMed: 30657780
• UniProt: Q9V2F3|DP2S_PYRAB DNA polymerase II small subunit (Gene Name=polB)