1VTY

Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs

• PDB DOI: https://doi.org/10.2210/pdb1VTY/pdb
• NAKB: 1VTY

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 1988-08-18 Released: 2011-07-13 
• Deposition Author(s): Coll, M., 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: 0.217 

Literature

Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs.

Coll, M., Wang, A.H., van der Marel, G.A., van Boom, J.H., Rich, A.

(1986) J Biomol Struct Dyn 4: 157-172

• PubMed: 3271437 
• DOI: https://doi.org/10.1080/07391102.1986.10506337
• Primary Citation of Related Structures:  
  1VTY


• PubMed Abstract: 
  

  The Z-DNA structure has been shown to form in two crystals made from self-complementary DNA hexamers d(CGTDCG) and d(CDCGTG) which contain thymine/2-aminoadenine (TD) base pairs. The latter structure has been solved and refined to 1.3 A resolution and it shows only small conformational changes due to the introduction of the TD base pairs in comparison with the structure of d(CG)3. Spectroscopic studies with these compounds demonstrate that DNA molecules containing 2-aminoadenine residues form Z-DNA slightly more easily than do those containing adenine nucleotides, but not as readily as the parent sequence containing only guanine-cytosine base pairs.

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.7 kDa 
• Atom Count: 326 
• 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(*CP*(NH2)AP*CP*GP*TP*G)-3')	A, B	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH2	C [auth A], E [auth B]	AMINO GROUP H2 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.86	α = 90
b = 31.04	β = 90
c = 44.76	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Coll, M., 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: 2018-10-10
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations