PDBsum entry 4jd8

DNA

PDB id: 4jd8

Contents

DNA/RNA

Ligands

0TN

RKP

Metals

__K

Waters ×95

PDB id:

4jd8

Name:

DNA

Title:

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

Structure:

DNA (5'-d( Ap Tp Gp Cp Ap T)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: DNA purchased from atdbio

Resolution:

1.16Å R-factor: 0.139 R-free: 0.162

Authors:

D.S.Cook,J.P.Hall,C.J.Cardin

Key ref:

J.P.Hall et al. (2013). X-ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering. J Am Chem Soc, 135, 12652-12659. PubMed id: 23875832 DOI: 10.1021/ja403590e

Date:

24-Feb-13 Release date: 24-Apr-13

Supersedes:

4e87

DNA/RNA chains

A-T-G-C-A-T 6 bases

A-T-G-C-A-T 6 bases

DOI no: 10.1021/ja403590e

J Am Chem Soc 135:12652-12659 (2013)

PubMed id: 23875832

X-ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering.

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

ABSTRACT

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.