3QRN image
Deposition Date 2011-02-18
Release Date 2011-10-19
Last Version Date 2023-11-01
Entry Detail
PDB ID:
3QRN
Keywords:
DNA
Title:
X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA)at high resolution
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.10 Å
R-Value Free:
0.12
R-Value Work:
0.10
R-Value Observed:
0.10
Space Group:
P 43 21 2
3QRN validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
Chain IDs:A
Chain Length:10
Number of Molecules:1
Biological Source:
Ligand Molecules
BA
RKL
Primary Citation
Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
Proc.Natl.Acad.Sci.USA 108 17610 17614 (2011)
PMID: 21969542 DOI: 10.1073/pnas.1108685108

Abstact

We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)(2)(dipyridophenazine)](2+) crystallizes in a 11 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.

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Primary Citation of related structures
3QF8