Structure of PDB 8vap Chain D Binding Site BS04

Receptor Information

>8vap Chain D (length=358) Species: 562 (Escherichia coli)

SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGK
TSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV
EDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVK
FLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPR
ALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALS
LVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAA
LGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEM
TLLRALAF

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 8vap Chain D Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vap Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): T52 D126
• Binding residue (residue number reindexed from 1): T51 D125
• Annotation score: 1

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0006260 DNA replication

Cellular Component

• GO:0009360 DNA polymerase III complex

External links

• PDB: RCSB:8vap, PDBe:8vap, PDBj:8vap
• PDBsum: 8vap
• PubMed: 38490435
• UniProt: P06710|DPO3X_ECOLI DNA polymerase III subunit tau (Gene Name=dnaX)