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

2ELG の概要

• エントリーDOI: 10.2210/pdb2elg/pdb
• 関連するPDBエントリー: 1DJ6 292d 293d 336d
• 分子名称: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3'), SPERMIDINE, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: d(cgcgcg)2, left-handed z-dna, spermidine, polyamine, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3861.56

構造登録者

Ohishi, H.,Tozuka, Y.,Zhou, D.Y.,Ishida, T.,Nakatani, K. (登録日: 2007-03-27, 公開日: 2008-04-01, 最終更新日: 2023-10-25)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1 Å)