1EG6

CRYSTAL STRUCTURE ANALYSIS OF D(CG(5-BRU)ACG) COMPLEXES TO A PHENAZINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG](2) with a topoisomerase poison in the presence of Co(2+) ions.

Thorpe, J.H.Hobbs, J.R.Todd, A.K.Denny, W.A.Charlton, P.Cardin, C.J.

(2000) Biochemistry 39: 15055-15061


  • PubMed Abstract: 
  • The structure of the duplex d[CG(5-BrU)ACG](2) bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 A resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel bin ...

    The structure of the duplex d[CG(5-BrU)ACG](2) bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 A resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co(2+) ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40 degrees, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co(2+) ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA ('hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.


    Organizational Affiliation

    Department of Chemistry, The University of Reading, Whiteknights, Reading RG6 6AD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3'A,B6N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

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Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
3CO
Query on 3CO

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Download CCD File 
A, B
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
BFA
Query on BFA

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Download CCD File 
B
9-BROMO-PHENAZINE-1-CARBOXYLIC ACID (2-DIMETHYLAMINO-ETHYL)-AMIDE
C17 H17 Br N4 O
QCANCQNKYBFYAC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 29.420α = 90.00
b = 53.440β = 90.00
c = 41.320γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CCP4data scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-03
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance