› 3u38

X-ray diffraction
2.13Å resolution

Intercalation of lambda-[Ru(phen)2(dppz)]2+ into d(CCGGTACCGG)2

Released:
DOI: 10.2210/pdb3u38/pdb
PDB entry 3u38 coloured by chain, front view.
PDB entry 3u38 coloured by chain, side view.
PDB entry 3u38 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes.
Niyazi H, Hall JP, O'Sullivan K, Winter G, Sorensen T, Kelly JM, Cardin CJ
Nat Chem 4 621-8 (2012)
PMID: 22824893

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-116954 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand RKP 2 x RKP
Ligand BA 1 x BA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P43212
Unit cell:
a: 52.56Å b: 52.56Å c: 32.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.232
Expression system: Not provided

Quick links

Citations

8 review citations

The path for metal complexes to a DNA target.
Komor et al. (2013)
7 more

3 mentions without citation

Molecular methods for assessment of non-covalent metallodrug-DNA interactions.
Kellett et al. (2019)
2 more