4GQJ

Complex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dppz)-(1,10-phenanthroline)4-Ru2]4+) bound to d(CGTACG)

  • Classification: DNA

  • Deposited: 2012-08-23 Released: 2014-03-05 
  • Deposition Author(s): Boer, D.R., Coll, M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.951 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes.

Boer, D.R.Wu, L.Lincoln, P.Coll, M.

(2014) Angew.Chem.Int.Ed.Engl. 53: 1949-1952

  • DOI: 10.1002/anie.201308070

  • PubMed Abstract: 
  • The crystal structure of the Δ,Δ enantiomer of the binuclear "light-switch" ruthenium complex [μ-(11,11'-bidppz)(1,10-phenanthroline)4  Ru2 ](4+) bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell-like compound inserts ...

    The crystal structure of the Δ,Δ enantiomer of the binuclear "light-switch" ruthenium complex [μ-(11,11'-bidppz)(1,10-phenanthroline)4  Ru2 ](4+) bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell-like compound inserts into the DNA stack through the extrusion of an AT base pair. The second dppz moiety recruits a neighboring DNA molecule, and the complex thus cross-links two adjacent duplexes by bridging their major grooves.


    Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixach 10, 08028 Barcelona (Spain); Institut de Biologia Molecular de Barcelona (CSIC), Baldiri Reixac 10, 08028 Barcelona (Spain).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')A,B6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RR2
Query on RR2

Download SDF File 
Download CCD File 
A
(mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium
C84 H50 N16 Ru2
BGOYAVNVNFHEQU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.951 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 85.429α = 90.00
b = 85.429β = 90.00
c = 85.429γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-23 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Boer, D.R., Coll, M.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release