› 4elt

X-ray diffraction
2.2Å resolution

Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines

Released:
DOI: 10.2210/pdb4elt/pdb
PDB entry 4elt coloured by chain, front view.
PDB entry 4elt coloured by chain, side view.
PDB entry 4elt coloured by chain, top view.
Source organisms:
Primary publication:
Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site.
Obeid S, Busskamp H, Welte W, Diederichs K, Marx A
Chem Commun (Camb) 48 8320-2 (2012)
PMID: 22766607

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-117423 (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:
DNA (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: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.95 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand 0R5 1 x 0R5
Ligand MG 3 x MG
Ligand GOL 9 x GOL
Ligand ACT 3 x ACT
Ligand EDO 1 x EDO
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 108.86Å b: 108.86Å c: 91.004Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.16 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Toolbox for Modified Aptamers.
Lapa et al. (2016)
11 other articles

1 mention without citation

Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency.
Zasedateleva et al. (2023)