3GOM

Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


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.USA 108: 17610-17614

  • DOI: 10.1073/pnas.1108685108
  • Primary Citation of Related Structures:  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 catio ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download SDF File 
Download CCD File 
A, B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.200α = 90.00
b = 23.800β = 110.01
c = 37.410γ = 90.00
Software Package:
Software NamePurpose
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
CrysalisProdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-02
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description