264D

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST 33258

• PDB DOI: https://doi.org/10.2210/pdb264D/pdb
• NAKB: 264D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-09-22 Released: 1995-03-31 
• Deposition Author(s): Vega, M.C., Garcia-Saez, I., Aymami, J., Eritja, R., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258.

Vega, M.C., Garcia Saez, I., Aymami, J., Eritja, R., Van der Marel, G.A., Van Boom, J.H., Rich, A., Coll, M.

(1994) Eur J Biochem 222: 721-726

• PubMed: 7517864 
• DOI: https://doi.org/10.1111/j.1432-1033.1994.tb18917.x
• Primary Citation of Related Structures:  
  264D


• PubMed Abstract: 
  

  The molecular structure of the DNA A-tract dodecamer d(CGCAAATTTGCG) complexed with the drug Hoechst 33258 has been determined by X-ray diffraction analysis. The Hoechst molecule binds in the DNA minor groove covering the sequence AATTT of the central A-tract, with the piperazine group close to one of the GC regions. The drug molecule makes two three-centered hydrogen bonds from the nitrogen atoms of the benzimidazole rings to the N3 and O2 atoms of the DNA bases. Although a high propeller twist is observed in the A-tract, only one unsymmetrical three-centered hydrogen bond is present in the DNA major groove. The structure is compared with other minor-groove-binding drug complexes and the influence of these drugs on DNA A-tracts is discussed.

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Organizational Affiliation: 

Departament de Biologia Molecular i Cel-lular, Centre d'Investigació i Desenvolupament-C.S.I.C., Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.75 kDa 
• Atom Count: 536 
• 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*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HT	C [auth B]	2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE C25 H24 N6 O INAAIJLSXJJHOZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.5	α = 90
b = 41.4	β = 90
c = 65.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-03-31 
Deposition Author(s): Vega, M.C., Garcia-Saez, I., Aymami, J., Eritja, R., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Coll, M.

Revision History  

• Version 1.0: 1995-03-31
  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: 2016-12-14
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations