Structure of PDB 1nom Chain A Binding Site BS01

Receptor Information

>1nom Chain A (length=242) Species: 10116 (Rattus norvegicus)

DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGL
KYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD
MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQ
LPSENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTI
NEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 1nom Chain A Residue 340

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1nom Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D190 D192 D256
• Binding residue (residue number reindexed from 1): D100 D102 D163
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D190 D192 D256
• Catalytic site (residue number reindexed from 1): D100 D102 D163
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:1nom, PDBe:1nom, PDBj:1nom
• PDBsum: 1nom
• PubMed: 8841120
• UniProt: P06766|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)