› 3t3f

X-ray diffraction
1.9Å resolution

Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP

Released:
DOI: 10.2210/pdb3t3f/pdb
PDB entry 3t3f coloured by chain, front view.
PDB entry 3t3f coloured by chain, side view.
PDB entry 3t3f coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Obeid S, Welte W, Diederichs K, Marx A
J Biol Chem 287 14099-108 (2012)
PMID: 22318723

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116909 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 60.94 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
5'-D(*AP*AP*AP*(3DR)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.82 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand GOL 13 x GOL
Ligand MG 4 x MG
Ligand NA 1 x NA
Ligand N5P 1 x N5P
Ligand FMT 4 x FMT
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3121
Unit cell:
a: 109.778Å b: 109.778Å c: 91.219Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.17 0.206
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.
Marx et al. (2020)
16 other articles

1 mention without citation

Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Obeid et al. (2012)