1OMK | pdb_00001omk

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

• PDB DOI: https://doi.org/10.2210/pdb1OMK/pdb
• NAKB: 1OMK

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-02-25 Released: 2003-11-04 
• Deposition Author(s): Schuerman, G., Van Hecke, K., Van Meervelt, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Work: 
  0.162 (DCC) 

Starting Model: experimental

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 D Biol Crystallogr 59: 1525-1528

• PubMed: 12876373 
• DOI: https://doi.org/10.1107/s0907444903012381
• Primary Citation Related Structures: 
  1OMK


• 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 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.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.16 kDa 
• Atom Count: 297 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*GP*(5IU)P*G)-3'	A, B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A], D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Work:  0.162 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.155	α = 90
b = 30.034	β = 90
c = 41.988	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-04 
Deposition Author(s): Schuerman, G., Van Hecke, K., Van Meervelt, L.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description