› 2xy5

X-ray diffraction
2.22Å resolution

Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus

Released:
DOI: 10.2210/pdb2xy5/pdb
PDB entry 2xy5 coloured by chain, front view.
PDB entry 2xy5 coloured by chain, side view.
PDB entry 2xy5 coloured by chain, top view.
Source organisms:
Primary publication:
Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair.
Kaul C, Müller M, Wagner M, Schneider S, Carell T
Nat Chem 3 794-800 (2011)
PMID: 21941252

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-115941 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 581 amino acids
Theoretical weight: 66.29 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.95 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.12 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, Z9N
Carbohydrate polymer
4 bound ligands:
Ligand SO4 4 x SO4
Ligand MRD 1 x MRD
Ligand CU1 1 x CU1
Ligand EDN 1 x EDN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 88.171Å b: 93.469Å c: 105.591Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.235
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures.
Herrmann A. (2014)
12 more

1 mention without citation

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications.
Burguera et al. (2023)