› 3n4n

X-ray diffraction
1.92Å resolution

Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one

Released:
DOI: 10.2210/pdb3n4n/pdb
PDB entry 3n4n coloured by chain, front view.
PDB entry 3n4n coloured by chain, side view.
PDB entry 3n4n coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
Magat Juan EC, Shimizu S, Ma X, Kurose T, Haraguchi T, Zhang F, Tsunoda M, Ohkubo A, Sekine M, Shibata T, Millington CL, Williams DM, Takénaka A
OpenAccess logo Nucleic Acids Res 38 6737-45 (2010)
PMID: 20554855

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116600 (preferred)
Entry contents:
2 distinct DNA molecules
Macromolecules (2 distinct):
5'-D(*CP*GP*CP*GP*AP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.82 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 6 nucleotides
Theoretical weight: 1.84 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand B7C 1 x B7C

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P3212
Unit cell:
a: 26.5Å b: 26.5Å c: 99Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.258 0.263
Expression system: Not provided

Quick links

Citations

5 citation in other articles

Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
Edwards et al. (2011)
4 more

1 mention without citation

Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
Magat Juan et al. (2010)