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PDBsum entry 6d4l
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References listed in PDB file
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Key reference
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Title
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Temperature-Induced replacement of phosphate proton with metal ion captured in neutron structures of a-Dna.
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Authors
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V.G.Vandavasi,
M.P.Blakeley,
D.A.Keen,
L.R.Hu,
Z.Huang,
A.Kovalevsky.
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Ref.
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Structure, 2018,
26,
1645.
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PubMed id
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Abstract
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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(CSe)CAC]2 containing 2'-SeCH3
modification on Cyt5 (CSe) 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.
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Secondary reference #1
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Title
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Generalized X-Ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
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Authors
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P.D.Adams,
M.Mustyakimov,
P.V.Afonine,
P.Langan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2009,
65,
567-573.
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PubMed id
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Headers
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