1VTW | pdb_00001vtw

AT Base Pairs Are Less Stable than GC Base Pairs in Z-DNA: The Crystal Structure of D(M(5)CGTAM(5)CG)

• PDB DOI: https://doi.org/10.2210/pdb1VTW/pdb
• NAKB: 1VTW

• Classification: DNA
• Mutation(s): No 


• Deposited: 1988-08-18 Released: 2011-07-13 
• Deposition Author(s): Wang, A.H.-J., Hakoshima, T., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Observed: 
  0.160 (Depositor) 

Literature

AT Base Pairs Are Less Stable than GC Base Pairs in Z-DNA: The Crystal Structure of d(m(5)CGTAm(5)CG)

Wang, A.H.-J., Hakoshima, T., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

(1984) Cell 37: 321-331

• PubMed: 6722876 
• DOI: https://doi.org/10.1016/0092-8674(84)90328-3
• Primary Citation Related Structures: 
  1VTW


• PubMed Abstract: 
  

  Two hexanucleoside pentaphosphates , 5-methyl and 5-bromo cytosine derivatives of d( CpGpTpApCpG ) have been synthesized, crystallized, and their three-dimensional structure solved. They both form left-handed Z-DNA and the methylated derivative has been refined to 1.2 A resolution. These are the first crystal Z-DNA structures that contain AT base pairs. The overall form of the molecule is very similar to that of the unmethylated or the fully methylated (dC-dG)3 hexamer although there are slight changes in base stacking. However, significant differences are found in the hydration of the helical groove. When GC base pairs are present, the helical groove is systematically filled with two water molecules per base pair hydrogen bonded to the bases. Both of these water molecules are not seen in the electron density map in the segments of the helix containing AT base pairs, probably because of solvent disorder. This could be one of the features that makes AT base pairs form Z-DNA less readily than GC base pairs.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.67 kDa 
• Atom Count: 244 
• Modeled 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*TP*AP*(CH3)CP*G)-3')	A, B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.91	α = 90
b = 30.43	β = 90
c = 44.96	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Wang, A.H.-J., Hakoshima, T., 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