5JEU

del-[Ru(phen)2(dppz)]2+ bound to d(TCGGCGCCGA) with Ba2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.113 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes.

Hall, J.P.Keane, P.M.Beer, H.Buchner, K.Winter, G.Sorensen, T.L.Cardin, D.J.Brazier, J.A.Cardin, C.J.

(2016) Nucleic Acids Res 44: 9472-9482

  • DOI: 10.1093/nar/gkw753
  • Primary Citation of Related Structures:  
    5JEU, 5JEV

  • PubMed Abstract: 
  • [Ru(phen) 2 (dppz)] 2+ has been studied since the 1990s due to its 'light-switch' properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding. The luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, and therefore is sensitive to changes in both binding site of the cation and chromophore orientation ...

    [Ru(phen) 2 (dppz)] 2+ has been studied since the 1990s due to its 'light-switch' properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding. The luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, and therefore is sensitive to changes in both binding site of the cation and chromophore orientation. The compound is also chiral, and there are distinct differences between the enantiomers in terms of the emission behaviour when bound to a variety of DNA sequences. Whilst a number of binary DNA-complex X-ray crystal structures are available, most include the Λ enantiomer and there is very little structural information about binding of the Δ enantiomer. Here, we present the first X-ray crystal structure of a Δ enantiomer bound to well-matched DNA, in the absence of the other, Λ enantiomer. We show how the binding site observed here can be related to a more general pattern of motifs in the crystallographic literature and propose that the Δ enantiomer can bind with five different binding modes, offering a new hypothesis for the interpretation of solution data.


    Organizational Affiliation

    Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK c.j.cardin@reading.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')A10synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0TN
Query on 0TN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Delta-Ru(phen)2(dppz) complex
C42 H26 N8 Ru
OYSRBLHMGIHFCB-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download Ideal Coordinates CCD File 
B [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.113 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.62α = 90
b = 48.62β = 90
c = 29.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2016-11-09
    Changes: Database references