› 5lfs

X-ray diffraction
1.85Å resolution

Lambda-[Ru(bpy)2(dppz)]2+ bound to brominated DNA

Released:
DOI: 10.2210/pdb5lfs/pdb
PDB entry 5lfs coloured by chain, front view.
PDB entry 5lfs coloured by chain, side view.
PDB entry 5lfs coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects.
Hall JP, Gurung SP, Henle J, Poidl P, Andersson J, Lincoln P, Winter G, Sorensen T, Cardin DJ, Brazier JA, Cardin CJ
Chemistry 23 4981-4985 (2017)
PMID: 28105682

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-118987 (preferred)
Entry contents:
2 distinct DNA molecules
Macromolecules (2 distinct):
DNA (5'-D(*GP*CP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*(CBR)P*GP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand BA 1 x BA
Ligand R1Z 1 x R1Z
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P6422
Unit cell:
a: 66.9Å b: 66.9Å c: 36.02Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.171 0.192
Expression system: Not provided

Quick links

Citations

6 citation in other articles

A three-in-one-bullet for oesophageal cancer: replication fork collapse, spindle attachment failure and enhanced radiosensitivity generated by a ruthenium(ii) metallo-intercalator.
Gill et al. (2018)
5 more

1 mention without citation

Photochemically active DNA-intercalating ruthenium and related complexes - insights by combining crystallography and transient spectroscopy.
Cardin et al. (2017)