ISDA

Entry Detail

PDB ID:

4III

Keywords:

DNA

Title:

Lambda-[Ru(TAP)2(11-Cl-dppz)] with a DNA decamer at atomic resolution

Biological Source:

Source Organism:

PDB Version:

Deposition Date:

2012-12-20

Release Date:

2013-07-17

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.02 Å

R-Value Free:

0.11

R-Value Work:

0.10

R-Value Observed:

0.10

Space Group:

P 43 21 2

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Description: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

RCZ

Primary Citation

Preferred orientation in an angled intercalation site of a chloro-substituted Lambda-[Ru(TAP)2(dppz)]2+ complex bound to d(TCGGCGCCGA)2.

Hall, J.P, Beer, H, Buchner, K, Cardin, D.J, Cardin, C.J.Show

Philos Trans A Math Phys Eng Sci 371 20120525 20120525 (2013)

PMID: 23776304 DOI: 10.1098/rsta.2012.0525

Abstact

The crystal structure of the ruthenium DNA 'light-switch' complex Λ-[Ru(TAP)2(11-Cl-dppz)](2+) (TAP=tetraazaphenanthrene, dppz=dipyrido[3,2-a':2',3'-c]phenazine) bound to the oligonucleotide duplex d(TCGGCGCCGA)2 is reported. The synthesis of the racemic ruthenium complex is described for the first time, and the racemate was used in this study. The crystal structure, at atomic resolution (1.0 Å), shows one ligand as a wedge in the minor groove, resulting in the 51(°) kinking of the double helix, as with the parent Λ-[Ru(TAP)2(dppz)](2+). Each complex binds to one duplex by intercalation of the dppz ligand and also by semi-intercalation of one of the orthogonal TAP ligands into a second symmetrically equivalent duplex. The 11-chloro substituent binds with the major component (66%) oriented with the 11-chloro substituent on the purine side of the terminal step of the duplex.

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Protein

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Primary Citation of related structures