4III

Lambda-[Ru(TAP)2(11-Cl-dppz)] with a DNA decamer at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.114 
  • R-Value Work: 0.101 

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Literature

Preferred orientation in an angled intercalation site of a chloro-substituted Lambda-[Ru(TAP)2(dppz)]2+ complex bound to d(TCGGCGCCGA)2.

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

(2013) Philos Trans A Math Phys Eng Sci 371: 20120525-20120525

  • DOI: 10.1098/rsta.2012.0525

  • PubMed Abstract: 
  • The crystal structure of the ruthenium DNA 'light-switch' complex Λ-[Ru(TAP)2(11-Cl-dppz)](2+) (TAP=tetraazaphenanthrene, dppz=dipyrido[3,2-a':2',3'-c]phenazine) bound to the oligonucleotide duplex d(TCGGCGCCGA)2 is reported. The synthesis of the rac ...

    The crystal structure of the ruthenium DNA 'light-switch' complex Λ-[Ru(TAP)2(11-Cl-dppz)](2+) (TAP=tetraazaphenanthrene, dppz=dipyrido[3,2-a':2',3'-c]phenazine) bound to the oligonucleotide duplex d(TCGGCGCCGA)2 is reported. The synthesis of the racemic ruthenium complex is described for the first time, and the racemate was used in this study. The crystal structure, at atomic resolution (1.0 Å), shows one ligand as a wedge in the minor groove, resulting in the 51(°) kinking of the double helix, as with the parent Λ-[Ru(TAP)2(dppz)](2+). Each complex binds to one duplex by intercalation of the dppz ligand and also by semi-intercalation of one of the orthogonal TAP ligands into a second symmetrically equivalent duplex. The 11-chloro substituent binds with the major component (66%) oriented with the 11-chloro substituent on the purine side of the terminal step of the duplex.


    Organizational Affiliation

    Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'A10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RCZ
Query on RCZ

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Download CCD File 
A
Ru(TAP)2(Cl-dppz) complex
C38 H21 Cl N12 Ru
CYFOMPOAWAYEMX-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.114 
  • R-Value Work: 0.101 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.340α = 90.00
b = 42.340β = 90.00
c = 39.630γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
GDAdata collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release