4MJ9

lambda-[Ru(TAP)2(dppz-10-Me)]2+ bound to a synthetic DNA oligomer

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2013-09-03 Released: 2014-09-24 
  • Deposition Author(s): Hall, J.P., Cardin, C.J.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.086 
  • R-Value Observed: 0.086 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru dppz Complexes to DNA

Hall, J.P., Beer, H., Buchner, K., Cardin, D.J., Cardin, C.J.

(2015) Organometallics 


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')10N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2J0
Query on 2J0
Download Ideal Coordinates CCD File 
B [auth A](10-methyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)
C39 H24 N12 Ru
SUPGJTRQQWHNCH-UHFFFAOYSA-N
BA
Query on BA
Download Ideal Coordinates CCD File 
C [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.086 
  • R-Value Observed: 0.086 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.27α = 90
b = 42.27β = 90
c = 39.67γ = 90
Software Package:
Software NamePurpose
GDAdata collection
SHELXCDphasing
SHELXEmodel building
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-05-13
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations