3QF8 | pdb_00003qf8

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

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2011-01-21 Released: 2011-10-19 
  • Deposition Author(s): Cardin, C.J., Hall, J.P.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.233 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 3.93 kDa 
  • Atom Count: 341 
  • Modeled Residue Count: 10 
  • Deposited Residue Count: 10 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'10N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.233 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.239α = 90
b = 42.239β = 90
c = 39.379γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
SHELXCDphasing
SHELXEmodel building
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata 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: 2013-06-26
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations