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PDBsum entry 1kd4
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References listed in PDB file
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Key reference
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Title
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Crystal structures of r(ggucacagccc)2.
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Authors
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V.Kacer,
S.A.Scaringe,
J.N.Scarsdale,
J.P.Rife.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
423-432.
[DOI no: ]
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PubMed id
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Abstract
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Crystals of small RNAs, which regularly diffract to very high resolution, can
often be readily obtained. Unfortunately, for some RNAs the conformations
adopted in the crystalline form are different from those found in solution. For
example, short RNAs that form hairpins in solution virtually never crystallize
thus; rather, they form duplexes. Nevertheless, these unintended structures have
contributed greatly to the understanding of RNA structure. In a similar
occurrence, the homodimer r(GGUCACAGCCC)(2) has been crystallized from an
11-mer/12-mer heteroduplex, r(GGCUGAAGUCCG)/r(GGUCACAGCCC). This surprising
phenomenon was observed under a variety of crystallization conditions. The
structure of the homoduplex was determined from crystals that differed in the
precipitant used and the type of metal present. In all cases, the resulting
homoduplexes contain ten base pairings, of which the central six are
non-canonical pairings. In two of the variants, ordered metal-binding sites were
observed: two equivalent octacoordinate Tl(+) sites in one and two equivalent
nanocoordinate Ba(2+) sites in another.
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Figure 1.
Figure 1 (a) Sequence of the heterodimer vkIX with strands A and
B. (b) Sequence of the homodimer vkIX-AA composed of strand A
only.
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Figure 5.
Figure 5 Metal coordination to vkIX-AA. Coordination bonds are
shown in blue and waters are shown as red spheres. (a) The two
Tl atoms (magenta) coordinated to vkIX-AA. (b) Detail of one of
the two Tl+ sites. Tl+ coordinates to N7 of A7, O2 and N3 of C4,
O4 of U3 and three water molecule O atoms. (c) The two Ba atoms
(magenta) coordinated to vkIX-AA. (d) Detail of one of the two
Ba^2+ sites. Ba^2+ coordinates to O6 of G8, O4 of U3, O6 of G2
and six water molecule O atoms. The image was created using the
program RIBBONS (Carson, 1991[128] [Carson, M. (1991). J. Appl.
Cryst. 24, 958-961.]-[129][bluearr.gif] ) and rendered using the
program POV-Ray ([130]http://www.povray.org ).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2003,
59,
423-432)
copyright 2003.
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Headers
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