4JD8

Racemic-[Ru(phen)2(dppz)]2+] bound to synthetic DNA at high resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

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Literature

X-ray Crystal Structure of rac-[Ru(phen)2dppz](2+) with d(ATGCAT)2 Shows Enantiomer Orientations and Water Ordering.

Hall, J.P., Cook, D., Morte, S.R., McIntyre, P., Buchner, K., Beer, H., Cardin, D.J., Brazier, J.A., Winter, G., Kelly, J.M., Cardin, C.J.

(2013) J Am Chem Soc 135: 12652-12659

  • DOI: https://doi.org/10.1021/ja403590e
  • Primary Citation of Related Structures:  
    4JD8

  • PubMed Abstract: 

    We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

    • Organizational Affiliation: 

    Chemistry Department, University of Reading, Whiteknights, Reading RG6 AD, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*GP*CP*AP*T)-3')
A, B
6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.55α = 90
b = 37.55β = 90
c = 54.371γ = 120
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description