ISDA

Deposition Date 2013-02-24

Release Date 2013-04-24

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4JD8

Keywords:

DNA

Title:

Racemic-[Ru(phen)2(dppz)]2+] bound to synthetic DNA at high resolution

Biological Source:

Source Organism:

(Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.16 Å

R-Value Free:

0.16

R-Value Work:

0.13

R-Value Observed:

0.13

Space Group:

P 31 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*TP*GP*CP*AP*T)-3')
Chain IDs:A, B
Chain Length:6
Number of Molecules:2
Biological Source:

Ligand Molecules

0TN

RKP

Primary Citation

X-ray Crystal Structure of rac-[Ru(phen)2dppz](2+) with d(ATGCAT)2 Shows Enantiomer Orientations and Water Ordering.

Hall, J.P, Cook, D, Morte, S.R, McIntyre, P, Buchner, K, Beer, H, Cardin, D.J, Brazier, J.A, Winter, G, Kelly, J.M, Cardin, C.J.Show

J.Am.Chem.Soc. 135 12652 12659 (2013)

PMID: 23875832 DOI: 10.1021/ja403590e

Abstact

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

Legend

Protein

Chemical

Disease

Primary Citation of related structures