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PDBsum entry 1nlc
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References listed in PDB file
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Key reference
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Title
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A crystallographic study of the binding of 13 metal ions to two related RNA duplexes.
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Authors
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E.Ennifar,
P.Walter,
P.Dumas.
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Ref.
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Nucleic Acids Res, 2003,
31,
2671-2682.
[DOI no: ]
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PubMed id
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Abstract
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Metal ions, and magnesium in particular, are known to be involved in RNA folding
by stabilizing secondary and tertiary structures, and, as cofactors, in RNA
enzymatic activity. We have conducted a systematic crystallographic analysis of
cation binding to the duplex form of the HIV-1 RNA dimerization initiation site
for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+,
Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+
and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the
two sequences are very similar, strong differences were found in their cation
binding properties. Divalent cations bind almost exclusively, as Mg2+, at
'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each
site. Notably, a given cation can have very different affinities for a priori
equivalent sites within the same molecule. Surprisingly, none of the two
hexammines used were able to efficiently replace hexahydrated magnesium.
Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA.
This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg
(H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation
exactly between the Watson-Crick sites of a G-C base pair after an obligatory
deprotonation of N1 of the guanine base. This extensive study of metal ion
binding using X-ray crystallography significantly enriches our knowledge on the
binding of middleweight or heavy metal ions to RNA, particularly compared with
magnesium.
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Headers
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