Structure of PDB 8vam Chain D Binding Site BS03

Receptor Information

>8vam Chain D (length=363) Species: 562 (Escherichia coli)

GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTR
GVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAAS
RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPP
EHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA
HEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDD
QALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRM
GVEMTLLRALAFH

Ligand information

• Ligand ID: BEF
• InChI: InChI=1S/Be.3FH/h;3*1H/q+2;;;/p-3
• InChIKey: OGIAHMCCNXDTIE-UHFFFAOYSA-K
• SMILES:
  OpenEye OEToolkits 1.5.0: [Be-](F)(F)F
  ACDLabs 10.04
  CACTVS 3.341: F[Be-](F)F
• Formula: Be F3
• Name: BERYLLIUM TRIFLUORIDE ION
• PDB chain: 8vam Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vam Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): K51 R215
• Binding residue (residue number reindexed from 1): K54 R218
• 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:8vam, PDBe:8vam, PDBj:8vam
• PDBsum: 8vam
• PubMed: 38490435
• UniProt: P06710|DPO3X_ECOLI DNA polymerase III subunit tau (Gene Name=dnaX)