1VTV

Molecular structure of (M5DC-DG)3: The role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA

• PDB DOI: https://doi.org/10.2210/pdb1VTV/pdb
• NAKB: 1VTV

• Classification: DNA
• Mutation(s): No 


• Deposited: 1989-01-10 Released: 2011-07-13 
• Deposition Author(s): Fujii, S., Wang, A.H.-J., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Observed: 0.156 

Literature

Molecular Structure of (m5dC-dG)3: The Role of the Methyl Group on 5-Methyl Cytosine in Stabilizing Z-DNA

Fujii, S., Wang, A.H.-J., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

(1982) Nucleic Acids Res 10: 7879-7892

• PubMed: 7155900 
• DOI: https://doi.org/10.1093/nar/10.23.7879
• Primary Citation of Related Structures:  
  1VTV


• PubMed Abstract: 
  

  The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. The presence of the methyl group has resulted in slight changes in the twist angle between successive base pairs and modification of some of the interatomic contacts. Methylation of cytosine in the C5 position is associated with a relative destabilization of the B-DNA structure and a stabilization through hydrophobic bonding of the Z-DNA structure.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.7 kDa 
• Atom Count: 252 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(CH3)CP*GP*(CH3)CP*GP*(CH3)CP*G)-3')	A, B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.76	α = 90
b = 30.57	β = 90
c = 45.42	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Fujii, S., Wang, A.H.-J., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations