› 2kfz

X-ray diffraction
2.03Å resolution

KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND ZINC ONLY

Released:
DOI: 10.2210/pdb2kfz/pdb
PDB entry 2kfz coloured by chain, front view.
PDB entry 2kfz coloured by chain, side view.
PDB entry 2kfz 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-115476 (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:
5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 1 x MG
1 modified residue:
Ligand US1 1 x US1

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P43
Unit cell:
a: 102.9Å b: 102.9Å c: 86.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.255
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

6 mentions without citation

Protein-RNA interactions: a structural analysis.
Jones et al. (2001)
5 more