1I47 | pdb_00001i47

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATSON-CRICK TYPE AND WOBBLE N4-METHOXYCYTIDINE/GUANOSINE BASE PAIRS IN B-DNA

• PDB DOI: https://doi.org/10.2210/pdb1I47/pdb
• NAKB: 1I47

• Classification: DNA
• Mutation(s): No 


• Deposited: 2001-02-20 Released: 2003-02-11 
• Deposition Author(s): Hossain, M.T., Hikima, T., Chatake, T., Tsunoda, M., Sunami, T., Ueno, Y., Matsuda, A., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.213 (Depositor), 0.207 (DCC) 

Starting Model: experimental

Literature

Crystallographic studies on damaged DNAs: III. N(4)-methoxycytosine can form both Watson-Crick type and wobbled base pairs in a B-form duplex

Hossain, M.T., Chatake, T., Hikima, T., Tsunoda, M., Sunami, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2001) J Biochem 130: 9-12

• PubMed: 11432773 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002967
• Primary Citation Related Structures: 
  1I3T, 1I47


• PubMed Abstract: 
  

  To investigate the mutation mechanism of purine transition in DNA damaged with methoxyamine, a DNA dodecamer with the sequence d(CGCGAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N(4)-methoxycytidine, has been synthesized and its crystal structure determined. Two dodecamers form a B-form duplex. Electron density maps clearly show that one of the two mo(4)C residues forms a pair with a guanine residue of the opposite strand, the geometry being the canonical Watson-Crick type, and that the other mo(4)C residue forms a wobble pair with the opposite guanine residue. These two pairings are ascribed to the tautomerization of the methoxylated cytosine moieties between the amino and imino forms.

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Organizational Affiliation: 
• Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.41 kDa 
• Atom Count: 571 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(C45)P*GP*CP*GP)-3'	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.213 (Depositor), 0.207 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.3	α = 90
b = 41.4	β = 90
c = 64.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-11 
Deposition Author(s): Hossain, M.T., Hikima, T., Chatake, T., Tsunoda, M., Sunami, T., Ueno, Y., Matsuda, A., Takenaka, A.

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description