5LFW

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

  • Classification: DNA
  • Organism(s): synthetic construct

  • 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: 1.28 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.141 

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:  5LFS, 5LFX

  • 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 compounds bind through ca ...

    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 NH2 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*G)-3')A4synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*(CBR)P*GP*GP*C)-3')C4synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RKP
Query on RKP

Download SDF File 
Download CCD File 
C
Lambda-Ru(phen)2(dppz) complex
C42 H26 N8 Ru
OYSRBLHMGIHFCB-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BT
Query on 5BT
C
NON-POLYMERC9 H12 Br N3 O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.141 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.340α = 90.00
b = 67.340β = 90.00
c = 35.790γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
SHELXCDphasing
XDSdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K019279/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M004635/1

Revision History 

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