1OMK

The Crystal Structure of d(CACG(5IU)G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].

Schuerman, G.Van Hecke, K.Van Meervelt, L.

(2003) Acta Crystallogr.,Sect.D 59: 1525-1528


  • PubMed Abstract: 
  • The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was d ...

    The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure.


    Organizational Affiliation

    Biomoleculaire Architectuur, Departement Chemie, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium.




Macromolecules

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

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Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
A, B
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 18.155α = 90.00
b = 30.034β = 90.00
c = 41.988γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SHELXLrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description