293D | pdb_0000293d

INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb293D/pdb
• NAKB: 293D

• Classification: DNA
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Interaction between the left-handed Z-DNA and polyamine-2. The crystal structure of the d(CG)3 and spermidine complex.

Ohishi, H., Nakanishi, I., Inubushi, K., van der Marel, G., van Boom, J.H., Rich, A., Wang, A.H., Hakoshima, T., Tomita, K.

(1996) FEBS Lett 391: 153-156

• PubMed: 8706905 
• DOI: https://doi.org/10.1016/0014-5793(96)00723-5
• Primary Citation Related Structures: 
  293D


• PubMed Abstract: 
  

  This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)-1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)3 and spermidine, but the binding mode of spermidine to the d(CG)3 molecule is different from that of the d(CG)3 and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)3 and its symmetrically related neighboring d(CG)3 molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)3 molecule, but not to its neighboring d(CG)3 molecule. In the crystal, the d(CG)3 molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)3 moiety with different binding modes from the case of the d(CG)3-PA(24) complex.

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Organizational Affiliation: 
• Osaka University of Pharmaceutical Sciences, Japan. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.86 kDa 
• Atom Count: 349 
• Modeled 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
SPD	C [auth A]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
MG	D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.93	α = 90
b = 31.23	β = 90
c = 44.64	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., Nakanishi, I., Inubushi, K., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J., Hakoshima, T., Tomita, K.

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