PDBe 3h8r

X-ray diffraction
1.77Å resolution

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system


Function and Biology Details

Reaction catalysed:
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA oxidative demethylase ALKBH2 Chain: A
Molecule details ›
Chain: A
Length: 209 amino acids
Theoretical weight: 23.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
  • Canonical: Q6NS38 (Residues: 56-261; Coverage: 79%)
Gene names: ABH2, ALKBH2
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(6MA)P*GP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.04 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P6522
Unit cell:
a: 78.08Å b: 78.08Å c: 228.71Å
α: 90° β: 90° γ: 120°
R R work R free
0.212 0.21 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided