› 3ajl

X-ray diffraction
2.7Å resolution

Crystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:guanosine Base-pair in B-DNA with DAPI

Released:
DOI: 10.2210/pdb3ajl/pdb
PDB entry 3ajl coloured by chain, front view.
PDB entry 3ajl coloured by chain, side view.
PDB entry 3ajl coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil.
Tsunoda M, Sakaue T, Naito S, Sunami T, Abe N, Ueno Y, Matsuda A, Takénaka A
J Nucleic Acids 2010 107289 (2010)
PMID: 20976303

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116065 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DAP 1 x DAP
Ligand MG 1 x MG
1 modified residue:
Ligand UFR 2 x UFR

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P212121
Unit cell:
a: 25.003Å b: 40.501Å c: 66.773Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.281
Expression system: Not provided

Quick links

Citations

3 review citations

Microenvironment-Cell Nucleus Relationship in the Context of Oxidative Stress.
Chittiboyina et al. (2018)
2 more

2 mentions without citation

Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil.
Tsunoda et al. (2010)
1 more