159D | pdb_0000159d

SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX

• PDB DOI: https://doi.org/10.2210/pdb159D/pdb
• NAKB: 159D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-02-10 Released: 1995-02-07 
• Deposition Author(s): Chen, X., Ramakrishnan, B., Rao, S.T., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.150 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.

Chen, X., Ramakrishnan, B., Rao, S.T., Sundaralingam, M.

(1994) Nat Struct Biol 1: 169-175

• PubMed: 7656035 
• DOI: https://doi.org/10.1038/nsb0394-169
• Primary Citation Related Structures: 
  159D


• PubMed Abstract: 
  

  Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove. The amides of each drug molecule are hydrogen bonded to the minor groove base atoms of only one DNA strand. The complex not only shows binding of two drug molecules, but the DNA duplex also exhibits striking low-high alternations in the helical twist angles, the sugar puckering and the phosphate conformations, providing the basis for a new model for an alternating B-DNA with a dinucleotide repeat.

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Organizational Affiliation: 
• Department of Chemistry, Ohio State University, Columbus 43210, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.87 kDa 
• Atom Count: 258 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3')	A	8	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMY	B [auth A]	DISTAMYCIN A C22 H27 N9 O4 UPBAOYRENQEPJO-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.150 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.93	α = 90
b = 27.93	β = 90
c = 57.67	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-07 
Deposition Author(s): Chen, X., Ramakrishnan, B., Rao, S.T., Sundaralingam, M.

Revision History  

• Version 1.0: 1995-02-07
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations