2D47

MOLECULAR STRUCTURE OF A COMPLETE TURN OF A-DNA

• PDB DOI: https://doi.org/10.2210/pdb2D47/pdb
• NAKB: 2D47

• Classification: DNA
• Mutation(s): No 


• Deposited: 1991-10-02 Released: 1991-10-02 
• Deposition Author(s): Verdaguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.177 

Literature

Molecular structure of a complete turn of A-DNA.

Verdaguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J., Subirana, J.A.

(1991) J Mol Biol 221: 623-635

• PubMed: 1920437 
• DOI: https://doi.org/10.1016/0022-2836(91)80077-8
• Primary Citation of Related Structures:  
  2D47


• PubMed Abstract: 
  

  We have determined the crystal structure of the dodecamer d(CCCCCGCGGGGG), showing for the first time a complete turn of A-DNA. It has average structural parameters similar to those determined in fibres. Nevertheless it shows a considerable local variation in structure which is in part associated with the presence of a bound spermine molecule. We conclude that the local DNA conformation does not only depend on the base sequence, but may be strongly modified upon interaction with other molecules. In particular, the CpG sequence, which is found in hypersensitive regions of the genome, appears to be able to easily change its conformation under external influences.

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Organizational Affiliation: 

Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.53 kDa 
• Atom Count: 607 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.177 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.2	α = 90
b = 45.2	β = 90
c = 65	γ = 120

Software Package:

Software Name	Purpose
NUCLSQ	refinement
MODIFIED	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-10-02 
Deposition Author(s): Verdaguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J., Subirana, J.A.

Revision History  

• Version 1.0: 1991-10-02
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations