3QRN

X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA)at high resolution

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2011-02-18 Released: 2011-10-19 
  • Deposition Author(s): Cardin, C.J., Hall, J.P.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.107 
  • R-Value Observed: 0.108 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.

Hall, J.P., O'Sullivan, K., Naseer, A., Smith, J.A., Kelly, J.M., Cardin, C.J.

(2011) Proc Natl Acad Sci U S A 108: 17610-17614

  • DOI: https://doi.org/10.1073/pnas.1108685108
  • Primary Citation of Related Structures:  
    3GOM, 3QF8, 3QRN

  • PubMed Abstract: 

    We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)(2)(dipyridophenazine)](2+) crystallizes in a 11 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.

    • Organizational Affiliation: 

    Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'10N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RKL
Query on RKL
Download Ideal Coordinates CCD File 
B [auth A]Ru(tap)2(dppz) complex
C38 H22 N12 Ru
PIKVAZQLFXBUSD-UHFFFAOYSA-N
BA
Query on BA
Download Ideal Coordinates CCD File 
C [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.107 
  • R-Value Observed: 0.108 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.32α = 90
b = 42.32β = 90
c = 39.87γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description