› 8xk9

X-ray diffraction
2.4Å resolution

ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

Released:
DOI: 10.2210/pdb8xk9/pdb
Model geometry
Fit model/data
PDB entry 8xk9 coloured by chain, front view.
PDB entry 8xk9 coloured by chain, side view.
PDB entry 8xk9 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.
Wen C, Wang G, Yang L, Chen T, Liu H, Gong W
J Mol Biol 436 168744 (2024)
PMID: 39147125

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-283120 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chains: A, D
Molecule details ›
Chains: A, D
Length: 539 amino acids
Theoretical weight: 60.8 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52028 (Residues: 296-833; Coverage: 65%)
Gene names: TTHA1054, polA
Sequence domains:
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3') Chains: C, F

Ligands and Environments

4 bound ligands:
Ligand MG 6 x MG
Ligand A1LWE 2 x A1LWE
Ligand PEG 2 x PEG
Ligand PO4 2 x PO4
2 modified residues:
Ligand DOC 2 x DOC
Ligand OMG 2 x OMG

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P43
Unit cell:
a: 105.986Å b: 105.986Å c: 191.722Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.218
Expression systems:
  • Escherichia coli
  • Not provided

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