› 8ctz

X-ray diffraction
2.32Å resolution

12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H

Released:
DOI: 10.2210/pdb8ctz/pdb
PDB entry 8ctz coloured by chain, front view.
PDB entry 8ctz coloured by chain, side view.
PDB entry 8ctz coloured by chain, top view.
Source organisms:
Primary publication:
Conformation and Pairing Properties of an O6-Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA.
Kellum AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M
Chem Res Toxicol (2022)
PMID: 35973057

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122482 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease H Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand GOL 4 x GOL
Ligand EDO 3 x EDO
Ligand ACT 2 x ACT
Ligand NA 1 x NA
Ligand K 2 x K
1 modified residue:
Ligand 6OG 2 x 6OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 59.506Å b: 66.492Å c: 69.182Å
α: 90° β: 107.97° γ: 90°
R-values:
R R work R free
0.199 0.195 0.265
Expression systems:
  • Escherichia coli
  • Not provided

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