454D

INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a photoactive rhodium complex intercalated into DNA.

Kielkopf, C.L.Erkkila, K.E.Hudson, B.P.Barton, J.K.Rees, D.C.

(2000) Nat.Struct.Mol.Biol. 7: 117-121

  • DOI: 10.1038/72385

  • PubMed Abstract: 
  • Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 A resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix ...

    Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 A resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix provides a rationale for the sequence specificity of rhodium intercalators. It also explains how intercalation in the center of an oligonucleotide modifies DNA conformation. The rhodium complex intercalates via the major groove where specific contacts are formed with the edges of the bases at the target site. The phi ligand is deeply inserted into the DNA base pair stack. The primary conformational change of the DNA is a doubling of the rise per residue, with no change in sugar pucker from B-form DNA. Based upon the five crystallographically independent views of an intercalated DNA helix observed in this structure, the intercalator may be considered as an additional base pair with specific functional groups positioned in the major groove.


    Organizational Affiliation

    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'A,B,C,D,E,F,G,H,I,J8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHM
Query on RHM

Download SDF File 
Download CCD File 
B, D, E, G, J
DELTA-ALPHA-RH[2R,9R-DIAMINO-4,7-DIAZADECANE]9,10-PHENANTHRENEQUINONE DIIMINE
RH(ME2TRIEN)PHI
C22 H27 N6 Rh
QQQIEFXIPDSOEX-IEPZTSNKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
A, B, C, D, E, F, G, H, I, J
DNA LINKINGC9 H12 I N2 O8 PDU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RHMKd: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.740α = 90.00
b = 23.980β = 93.24
c = 96.520γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SHELXL-97refinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance