6d54 | pdb_00006d54

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

spinqualitylabelsall models 6d54, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6d54 is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Hybrid , Neutron Diffraction , X-ray diffraction, Resolution 1.65Å Ligands: CSL, DOD, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 Mg(2+) upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature. Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.,Vandavasi VG, Blakeley MP, Keen DA, Hu LR, Huang Z, Kovalevsky A Structure. 2018 Aug 16. pii: S0969-2126(18)30289-2. doi:, 10.1016/j.str.2018.08.001. PMID:30244969 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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