6w2m

X-ray diffraction
2Å resolution

Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA

Released:

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-120797 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 38.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
Template Strand Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: synthetic construct
Expression system: Not provided
Primer Strand Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
Downstream Primer Strand Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 50.751Å b: 80.462Å c: 55.612Å
α: 90° β: 107.75° γ: 90°
R-values:
R R work R free
0.196 0.193 0.238
Expression systems:
  • Escherichia coli
  • Not provided