Structure of PDB 3gij Chain B Binding Site BS05

Receptor Information

>3gij Chain B (length=341) Species: 273057 (Saccharolobus solfataricus P2)

GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 3gij Chain B Residue 1416

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gij Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): D1007 F1008 D1105
• Binding residue (residue number reindexed from 1): D7 F8 D105
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0042276 error-prone translesion synthesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3gij, PDBe:3gij, PDBj:3gij
• PDBsum: 3gij
• PubMed: 19446528
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)