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PDBsum entry 1dnx
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DNA-RNA hybrid
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PDB id
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1dnx
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References listed in PDB file
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Key reference
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Title
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Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of a-Form nucleic acid duplexes.
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Authors
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H.Robinson,
Y.G.Gao,
R.Sanishvili,
A.Joachimiak,
A.H.Wang.
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Ref.
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Nucleic Acids Res, 2000,
28,
1760-1766.
[DOI no: ]
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PubMed id
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Abstract
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Magnesium ions play important roles in the structure and function of nucleic
acids. Whereas the tertiary folding of RNA often requires magnesium ions binding
to tight places where phosphates are clustered, the molecular basis of the
interactions of magnesium ions with RNA helical regions is less well understood.
We have refined the crystal structures of four decamer oligonucleotides,
d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with
bound hexahydrated magnesium ions at high resolution. The structures reveal that
A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode
has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of
guanine bases via hydrogen bonds. Our crystallographic observations are
consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+),
a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode
involves the binding of the ion to phosphates, bridging across the outer mouth
of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most
negative electrostatic potential regions of A-form duplexes. We propose that
these two binding modes are important in the global charge neutralization, and
therefore stability, of A-form duplexes.
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Headers
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