4JD8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

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

  • DOI: 10.1021/ja403590e

  • PubMed 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 wi ...

    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.


    Organizational Affiliation

    Chemistry Department, University of Reading, Whiteknights, Reading RG6 AD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*GP*CP*AP*T)-3')A,B6N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
RKP
Query on RKP

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Download CCD File 
B
Lambda-Ru(phen)2(dppz) complex
C42 H26 N8 Ru
OYSRBLHMGIHFCB-UHFFFAOYSA-N
 Ligand Interaction
0TN
Query on 0TN

Download SDF File 
Download CCD File 
B
Delta-Ru(phen)2(dppz) complex
C42 H26 N8 Ru
OYSRBLHMGIHFCB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.138 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 37.550α = 90.00
b = 37.550β = 90.00
c = 54.371γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
Aimlessdata scaling
GDAdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references