5LFX

Lambda-[Ru(phen)2(dppz-11,12-Me)]2+ bound to a short substituted DNA sequence

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2016-07-04 Released: 2017-02-15 
  • Deposition Author(s): Hall, J.P., Cardin, C.J.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects.

Hall, J.P.Gurung, S.P.Henle, J.Poidl, P.Andersson, J.Lincoln, P.Winter, G.Sorensen, T.Cardin, D.J.Brazier, J.A.Cardin, C.J.

(2017) Chemistry 23: 4981-4985

  • DOI: 10.1002/chem.201605508
  • Primary Citation of Related Structures:  
    5LFX, 5LFW, 5LFS

  • PubMed Abstract: 
  • X-ray crystal structures of three Λ-[Ru(L) 2 dppz] 2+ complexes (dppz=dipyridophenazine; L=1,10-phenanthroline (phen), 2,2'-bipyridine (bpy)) bound to d((5BrC)GGC/GCCG) showed the compounds intercalated at a 5'-CG-3' step. The ...

    X-ray crystal structures of three Λ-[Ru(L) 2 dppz] 2+ complexes (dppz=dipyridophenazine; L=1,10-phenanthroline (phen), 2,2'-bipyridine (bpy)) bound to d((5BrC)GGC/GCCG) showed the compounds intercalated at a 5'-CG-3' step. The compounds bind through canted intercalation, with the binding angle determined by the guanine NH 2 group, in contrast to symmetrical intercalation previously observed at 5'-TA-3' sites. This result suggests that canted intercalation is preferred at 5'-CG-3' sites even though the site itself is symmetrical, and we hypothesise that symmetrical intercalation in a 5'-CG-3' step could give rise to a longer luminescence lifetime than canted intercalation.


    Organizational Affiliation

    Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(CBR)P*GP*GP*C)-3')C4synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*CP*G)-3')A4synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      9ZQ
      Query on 9ZQ

      Download CCD File 
      A
      Ru(phen)2(dppz-11,12-Me2)
      C44 H30 N8 Ru
      SWTHIMQOVCZKDV-UHFFFAOYSA-N
       Ligand Interaction
      BA
      Query on BA

      Download CCD File 
      A
      BARIUM ION
      Ba
      XDFCIPNJCBUZJN-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.56 Å
      • R-Value Free: 0.192 
      • R-Value Work: 0.144 
      • R-Value Observed: 0.146 
      • Space Group: P 64 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 67.72α = 90
      b = 67.72β = 90
      c = 35.85γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      Aimlessdata scaling
      SHELXCDphasing
      xia2data reduction

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K019279/1
      Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M006435/1

      Revision History 

      • Version 1.0: 2017-02-15
        Type: Initial release
      • Version 1.1: 2017-04-19
        Changes: Database references
      • Version 1.2: 2017-08-30
        Changes: Author supporting evidence