4E7Y

Lambda-[Ru(phen)2(dppz)]2+ Bound to CCGGATCCGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of lambda-[Ru(phen)2(dppz)]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes.

Niyazi, H.Hall, J.P.O'Sullivan, K.Winter, G.Sorensen, T.Kelly, J.M.Cardin, C.J.

(2012) Nat Chem 4: 621-628

  • DOI: 10.1038/nchem.1397
  • Primary Citation of Related Structures:  3U38

  • PubMed Abstract: 
  • The ruthenium complex [Ru(phen)(2)(dppz)](2+) (where phen is phenanthroline and dppz dipyridophenazine is known as a 'light switch' complex because its luminescence in solution is significantly enhanced in the presence of DNA. This property is poised ...

    The ruthenium complex [Ru(phen)(2)(dppz)](2+) (where phen is phenanthroline and dppz dipyridophenazine is known as a 'light switch' complex because its luminescence in solution is significantly enhanced in the presence of DNA. This property is poised to serve in diagnostic and therapeutic applications, but its binding mode with DNA needs to be elucidated further. Here, we describe the crystal structures of the Λ enantiomer bound to two oligonucleotide duplexes. The dppz ligand intercalates symmetrically and perpendicularly from the minor groove of the d(CCGGTACCGG)(2) duplex at the central TA/TA step, but not at the central AT/AT step of d(CCGGATCCGG)(2). In both structures, however, a second ruthenium complex links the duplexes through the combination of a shallower angled intercalation into the C(1)C(2)/G(9)G(10) step at the end of the duplex, and semi-intercalation into the G(3)G(4) step of an adjacent duplex. The TA/TA specificity of the perpendicular intercalation arises from the packing of phenanthroline ligands against the adenosine residue.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'A10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RKP
Query on RKP

Download SDF File 
Download CCD File 
A
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.720α = 90.00
b = 47.720β = 90.00
c = 34.660γ = 90.00
Software Package:
Software NamePurpose
SHELXCDphasing
SHELXEmodel building
GDAdata collection
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2013-04-24
    Type: Non-polymer description
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description