PDBsum entry 6d4l

DNA

PDB id: 6d4l

Contents

DNA/RNA

Ligands

DOD ×29

Metals

_MG

PDB id:

6d4l

Name:

DNA

Title:

Joint x-ray/neutron structure of DNA oligonucleotide d(gtggccac)2 with 2'-sech3 modification on cyt5

Structure:

DNA (5'-d( Gp Tp Gp Gp (Csl)p Cp Ap C)-3'). Chain: a. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

1.56Å R-factor: 0.242 R-free: 0.276

Authors:

A.Kovalevsky,Z.Huang,V.G.Vandavasi

Key ref:

V.G.Vandavasi et al. (2018). Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA. Structure, 26, 1645. PubMed id: 30244969

Date:

18-Apr-18 Release date: 17-Oct-18

DNA/RNA chain

G-T-G-G-CSL-C-A-C 8 bases

Structure 26:1645 (2018)

PubMed id: 30244969

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.

V.G.Vandavasi, M.P.Blakeley, D.A.Keen, L.R.Hu, Z.Huang, A.Kovalevsky.

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^Se)CAC]₂ containing 2'-SeCH₃ modification on Cyt5 (C^Se) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg²⁺ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.