8A71

Crystal structure of right-handed Z-DNA containing 2'-deoxy-L-ribose in complex with the polyamine cadaverine and potassium cations at ultrahigh resolution

8A71 の概要

• エントリーDOI: 10.2210/pdb8a71/pdb
• 関連するPDBエントリー: 4hif 4hig 4r15 5jzq 7atg
• 分子名称: Right-handed Z-DNA, 5-azaniumylpentylazanium, POTASSIUM ION, ... (4 entities in total)
• 機能のキーワード: z-dna, dna, right-handed z-dna, cadaverine, potassium, cadaverinium cation, biogenic polyamines, 2-deoxy-l-ribose
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3763.70

構造登録者

Drozdzal, P.,Manszewski, T.,Gilski, M.,Brzezinski, K.,Jaskolski, M. (登録日: 2022-06-20, 公開日: 2023-02-22, 最終更新日: 2024-02-07)

主引用文献

Drozdzal, P.,Manszewski, T.,Gilski, M.,Brzezinski, K.,Jaskolski, M.
Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.
Acta Crystallogr D Struct Biol, 79:133-139, 2023

PubMed Abstract: The self-complementary L-d(CGCGCG) purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder.

PubMed: 36762859
DOI: 10.1107/S2059798322011937

実験手法

X-RAY DIFFRACTION (0.69 Å)