› 2kzm

X-ray diffraction
2.6Å resolution

KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE

Released:
DOI: 10.2210/pdb2kzm/pdb
PDB entry 2kzm coloured by chain, front view.
PDB entry 2kzm coloured by chain, side view.
PDB entry 2kzm coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli.
Brautigam CA, Sun S, Piccirilli JA, Steitz TA
Biochemistry 38 696-704 (1999)
PMID: 9888810

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 domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115513 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 605 amino acids
Theoretical weight: 68.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00582 (Residues: 324-928; Coverage: 65%)
Gene names: JW3835, b3863, polA, resA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*CP*TP*TP*A*CP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 8 nucleotides
Theoretical weight: 2.4 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 1 x MN
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P43
Unit cell:
a: 102.6Å b: 102.6Å c: 86.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.243
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
5 more

1 mention without citation

Prediction of functional sites by analysis of sequence and structure conservation.
Panchenko et al. (2004)