2ELG

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

Summary for 2ELG

• Entry DOI: 10.2210/pdb2elg/pdb
• Related: 1DJ6 292d 293d 336d
• Descriptor: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3'), SPERMIDINE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: d(cgcgcg)2, left-handed z-dna, spermidine, polyamine, dna
• Total number of polymer chains: 2
• Total formula weight: 3861.56

Authors

Ohishi, H.,Tozuka, Y.,Zhou, D.Y.,Ishida, T.,Nakatani, K. (deposition date: 2007-03-27, release date: 2008-04-01, Last modification date: 2023-10-25)

Primary citation

Ohishi, H.,Tozuka, Y.,Da-Yang, Z.,Ishida, T.,Nakatani, K.
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
Biochem.Biophys.Res.Commun., 358:24-28, 2007

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.

PubMed: 17467661
DOI: 10.1016/j.bbrc.2007.04.026

Experimental method

X-RAY DIFFRACTION (1 Å)