4GQJ | pdb_00004gqj

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
  • Mutation(s): No 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RR2Click on this verticalbar to view details

This is version 1.2 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: https://doi.org/10.1002/anie.201308070
  • Primary Citation of Related Structures:  
    4GQJ

  • 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 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 nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
A, B
6N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RR2
Query on RR2
Download Ideal Coordinates CCD File 
C [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.429α = 90
b = 85.429β = 90
c = 85.429γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
SHELXSphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RR2Click on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-03-13
    Changes: Source and taxonomy, Structure summary