2ELG | pdb_00002elg

The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 degree celsius

• PDB DOI: https://doi.org/10.2210/pdb2ELG/pdb
• NAKB: 2ELG

• Classification: DNA
• Mutation(s): No 


• Deposited: 2007-03-27 Released: 2008-04-01 
• Deposition Author(s): Ohishi, H., Tozuka, Y., Zhou, D.Y., Ishida, T., Nakatani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.232 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

The rare crystallographic structure of d(CGCGCG)(2): The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C

Ohishi, H., Tozuka, Y., Da-Yang, Z., Ishida, T., Nakatani, K.

(2007) Biochem Biophys Res Commun 358: 24-28

• PubMed: 17467661 
• DOI: https://doi.org/10.1016/j.bbrc.2007.04.026
• Primary Citation Related Structures: 
  2ELG


• PubMed Abstract: 
  

  Several crystal structure analyses of complexes of synthetic polyamine compounds, including N(1)-(2-(2-aminoethylamino))ethyl)ethane-1,2-diamine PA(222) and N(1)-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA(2222), and left-handed Z-DNA d(CGCGCG)(2) have been reported. However, until now, there have been no examples of naturally occurring polyamines bound to the minor groove of the left-handed Z-DNA of d(CGCGCG)(2) molecule. We have found that spermidine, a natural polyamine, is connected to the minor groove of left-handed Z-DNA of d(CGCGCG)(2) molecule in a crystalline complex grown at 10 degrees C. The electron density of the DNA molecule was clear enough to determine that the spermidine was connected in the minor groove of two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2). This is the first example that a spermidine molecule can form a bridge conformation between two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2) in the minor groove.

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Organizational Affiliation: 
• Osaka University of Pharmaceutical Sciences, 4-20-1, Nasahara, Takatsuki, Osaka 569-1094, Japan. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.86 kDa 
• Atom Count: 321 
• 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(*DCP*DGP*DCP*DGP*DCP*DG)-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], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.232 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.847	α = 90
b = 30.988	β = 90
c = 44.022	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MERLOT	phasing
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Ohishi, H., Tozuka, Y., Zhou, D.Y., Ishida, T., Nakatani, K.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description