292D

INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE:THE CRYSTAL STRUCTURE OF THE D(CG)3 AND N-(2-AMINOETHYL)-1,4-DIAMINOBUTANE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb292D/pdb
• NAKB: 292D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1991-10-09 Released: 1996-12-02 
• Deposition Author(s): Ohishi, H., Kunisawa, S., Van Der Marel, G., Van Boom, J.H., Rich, A., Wang, A.H.-J., Tomita, K., Hakoshima, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Observed: 0.161 

Literature

Interaction between the left-handed Z-DNA and polyamine. The crystal structure of the d(CG)3 and N-(2-aminoethyl)-1,4-diamino-butane complex.

Ohishi, H., Kunisawa, S., van der Marel, G., van Boom, J.H., Rich, A., Wang, A.H., Tomita, K., Hakoshima, T.

(1991) FEBS Lett 284: 238-244

• PubMed: 2060642 
• DOI: https://doi.org/10.1016/0014-5793(91)80694-x
• Primary Citation of Related Structures:  
  292D


• PubMed Abstract: 
  

  The DNA fragment d(CG)3 was co-crystallized with N-(2-aminoethyl)-1,4-diaminobutane (PA(24], a chemically synthesized polyamine. The complex crystal contained one polyamine, 3 magnesium cations and one sodium cation per duplex of d(CG)3, and well diffracted the X-ray intensities up to 1.0 A resolution. The d(CG)3 took a left-handed Z-DNA conformation, and the PA(24) molecule electrostatically interacted with the phosphate groups of the d(CG)3 duplex.

---

Organizational Affiliation: 

Osaka University of Pharmaceutical Sciences, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.85 kDa 
• Atom Count: 333 
• 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*GP*CP*GP*CP*G)-3')	A, B	6	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P24	C [auth A]	1-(AMINOETHYL)AMINO-4-AMINOBUTANE C6 H17 N3 VRPPEXGZBZBARW-UHFFFAOYSA-N
MG	D [auth A], E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.94	α = 90
b = 31.23	β = 90
c = 44.55	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-02 
Deposition Author(s): Ohishi, H., Kunisawa, S., Van Der Marel, G., Van Boom, J.H., Rich, A., Wang, A.H.-J., Tomita, K., Hakoshima, T.

Revision History  

• Version 1.0: 1996-12-02
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description