5WSP

Crystal structure of DNA3 duplex

5WSP の概要

• エントリーDOI: 10.2210/pdb5wsp/pdb
• 関連するPDBエントリー: 5WSQ 5WSR 5WSS
• 分子名称: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3'), STRONTIUM ION (3 entities in total)
• 機能のキーワード: dna duplex, t:t pair, dna
• 由来する生物種: unidentified
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 2506.21

構造登録者

Gan, J.H.,Liu, H.H. (登録日: 2016-12-08, 公開日: 2017-02-08, 最終更新日: 2024-03-20)

主引用文献

Liu, H.H.,Cai, C.,Haruehanroengra, P.,Yao, Q.Q.,Chen, Y.Q.,Yang, C.,Luo, Q.,Wu, B.X.,Li, J.X.,Ma, J.B.,Sheng, J.,Gan, J.H.
Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex
Nucleic Acids Res., 45:2910-2918, 2017

PubMed Abstract: Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII. Our structures suggest that both C-T and T-T pairs are flexible in interacting with the HgII ion with various binding modes including N3-HgII-N3, N4-HgII-N3, O2-HgII-N3 and N3-HgII-O4. Our studies also reveal that the overall conformations of the C-HgII-T and T-HgII-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C-HgII-T or T-HgII-T containing DNA nanodevices in the future.

PubMed: 27998930
DOI: 10.1093/nar/gkw1296

実験手法

X-RAY DIFFRACTION (1.502 Å)