5NBE image
Entry Detail
PDB ID:
5NBE
Keywords:
DNA
Title:
[Ru(TAP)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2
Biological Source:
Source Organism:
synthetic construct
PDB Version:
Deposition Date:
2017-03-01
Release Date:
2018-03-21
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.51 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 43 21 2
5NBE validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (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:synthetic construct
Ligand Molecules
BA
KSB
Primary Citation
X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes.
Chemistry 24 15859 15867 (2018)
PMID: 30063271 DOI: 10.1002/chem.201803021

Abstact

The new complexes [Ru(TAP)2 (11-CN-dppz)]2+ , [Ru(TAP)2 (11-Br-dppz)]2+ and [Ru(TAP)2 (11,12-diCN-dppz)]2+ are reported. The addition of nitrile substituents to the dppz ligand of the DNA photo-oxidising complex [Ru(TAP)2 (dppz)]2+ promote π-stacking interactions and ordered binding to DNA, as shown by X-ray crystallography. The structure of Λ-[Ru(TAP)2 (11-CN-dppz)]2+ with the DNA duplex d(TCGGCGCCGA)2 shows, for the first time with this class of complex, a closed intercalation cavity with an AT base pair at the terminus. The structure obtained is compared to that formed with the 11-Br and 11,12-dinitrile derivatives, highlighting the stabilization of syn guanine by this enantiomer when the terminal base pair is GC. In contrast the AT base pair has the normal Watson-Crick orientation, highlighting the difference in charge distribution between the two purine bases and the complementarity of the dppz-purine interaction. The asymmetry of the cavity highlights the importance of the purine-dppz-purine stacking interaction.

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Primary Citation of related structures
5NBE