6D4L

Joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5

6D4L の概要

• エントリーDOI: 10.2210/pdb6d4l/pdb
• 分子名称: DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3'), MAGNESIUM ION (3 entities in total)
• 機能のキーワード: dna oligonucleotide selenium modification, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 2544.90

構造登録者

Kovalevsky, A.,Huang, Z.,Vandavasi, V.G. (登録日: 2018-04-18, 公開日: 2018-10-17, 最終更新日: 2023-10-04)

主引用文献

Vandavasi, V.G.,Blakeley, M.P.,Keen, D.A.,Hu, L.R.,Huang, Z.,Kovalevsky, A.
Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.
Structure, 26:1645-, 2018

PubMed Abstract: Nucleic acids can fold into well-defined 3D structures that help determine their function. Knowing precise nucleic acid structures can also be used for the design of nucleic acid-based therapeutics. However, locations of hydrogen atoms, which are key players of nucleic acid function, are normally not determined with X-ray crystallography. Accurate determination of hydrogen atom positions can provide indispensable information on protonation states, hydrogen bonding, and water architecture in nucleic acids. Here, we used neutron crystallography in combination with X-ray diffraction to obtain joint X-ray/neutron structures at both room and cryo temperatures of a self-complementary A-DNA oligonucleotide d[GTGG(C)CAC] containing 2'-SeCH modification on Cyt5 (C) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.

PubMed: 30244969
DOI: 10.1016/j.str.2018.08.001

実験手法

NEUTRON DIFFRACTION (2 Å)
X-RAY DIFFRACTION (1.56 Å)