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PDBsum entry 373d
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Ribonucleic acid
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PDB id
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373d
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References listed in PDB file
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Key reference
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Title
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Metals, Motifs, And recognition in the crystal structure of a 5s rrna domain.
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Authors
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C.C.Correll,
B.Freeborn,
P.B.Moore,
T.A.Steitz.
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Ref.
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Cell, 1997,
91,
705-712.
[DOI no: ]
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PubMed id
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Abstract
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Two new RNA structures portray how non-Watson-Crick base pairs and metal ions
can produce a unique RNA shape suitable for recognition by proteins. The crystal
structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer
encompassing an internal loop E have been determined at 3.0 and 1.5 A,
respectively. This loop E region is distorted by three "cross-strand purine
stacks" and three novel, water-mediated noncanonical base pairs and stabilized
by a four metal ion zipper. These features give its minor groove a unique
hydrogen-bonding surface and make the adjacent major groove wide enough to
permit recognition by the ribosomal protein L25, which is expected to bind to
this surface.
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Figure 2.
Figure 2. The Cross-Strand Purine Stack(A) A cross-strand A
stack showing A104 from one strand in blue stacked on A73 of the
other strand in yellow. The position of the kink at the β and
γ angles of the yellow backbone is indicated.(B) Nucleotide
sequences of the six observed cross-strand A stacks ([42, 32, 39
and 11]) and the consensus for bulged and nonbulged A stacks.
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Figure 5.
Figure 5. Stereo Diagrams of Metal Sites A through E(A) A
frequently observed G•G metal ion binding site showing the
involvement of water in outer-sphere coordination.(B) The
“metal ion zipper” in the narrow major groove of loop E. The
two strands are in green and blue.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1997,
91,
705-712)
copyright 1997.
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Secondary reference #1
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Title
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Conformational features of the four successive non-Watson-Crick base pairs in RNA duplex.
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Authors
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S.Fujii,
Y.Tanaka,
S.Uesugi,
T.Tanaka,
T.Sakata,
H.Hiroaki.
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Ref.
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Nucleic Acids Symp Ser, 1992,
27,
63-64.
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PubMed id
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Secondary reference #2
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Title
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Molecular structure of extraordinarily stable RNA: model building and x-Ray analysis.
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Authors
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S.Fujii,
Y.Tanaka,
K.Tomita,
T.Sakata,
H.Hiroaki,
T.Tanaka,
S.Uesugi.
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Ref.
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Nucleic Acids Symp Ser, 1991,
25,
181-182.
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PubMed id
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