6RNL image
Deposition Date 2019-05-09
Release Date 2019-08-28
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6RNL
Keywords:
Title:
L-[Ru(TAP)2(dppz)]2+ bound to the G-quadruplex forming sequence d(TAGGGTT)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.88 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 65
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*GP*GP*GP*TP*T)-3')
Chain IDs:A, B, C, D
Chain Length:7
Number of Molecules:4
Biological Source:synthetic construct
Primary Citation
Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography.
Chem.Commun.(Camb.) 55 9116 9119 (2019)
PMID: 31298665 DOI: 10.1039/c9cc04316k

Abstact

Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed from terminal T·A and T·T mismatched pairs. A third shows kinking by a TAP ligand between T·T linkages, while the fourth shows sandwiching of a dppz ligand between a T·A/T·A quadruplex and a T·T mismatch, stabilised by an additional T·A base pair stacking interaction on a TAP surface. Overall, the structure shows an unexpected affinity for thymine, and suggests models for G-quadruplex loop binding.

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