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Title
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Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.
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Authors
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E.Westhof,
M.Sundaralingam.
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Ref.
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Biochemistry, 1986,
25,
4868-4878.
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PubMed id
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Abstract
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The structure of yeast phenylalanine transfer RNA in the monoclinic form has
been further refined by using the restrained least-squares method of Hendrickson
and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at
least 3 times their standard deviations, the R factor is 16.8%. The variation of
the atomic temperature factors along the sequence indicates that the major
flexibility regions are the amino acid and anticodon stems. The two strands of
the amino acid helix exhibit large differential temperature factors, suggesting
partial uncoiling or melting of the helix. In this work, the occupancy of all
atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well
as U33 and G37 of the anticodon loop have occupancies around 70%, indicating
some local disorder or large-scale mobility at these positions. One hundred
fifteen solvent molecules, including five magnesium ions, were found in
difference maps. The role of several water molecules is clearly related to the
stabilization of the secondary and tertiary interactions. The gold sites, which
were not previously discussed, are described and show an energetically favored
binding mode similar to that of cobalt and nickel complexes with nucleotides.
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