› 4hqi

X-ray diffraction
1.7Å resolution

Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex

Released:
DOI: 10.2210/pdb4hqi/pdb
PDB entry 4hqi coloured by chain, front view.
PDB entry 4hqi coloured by chain, side view.
PDB entry 4hqi coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP
Nucleic Acids Res 41 7566-76 (2013)
PMID: 23748954

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-117607 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
Short modified nucleic acids Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.83 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SPM 1 x SPM
Ligand SR 1 x SR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D, APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 26.384Å b: 36.774Å c: 77.653Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.262 0.259 0.298
Expression system: Not provided

Quick links

Citations

1 review citation

Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery.
Berdis A. (2022)
4 other articles

2 mentions without citation

Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
Kowal et al. (2013)
1 more