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. Author manuscript; available in PMC: 2009 Feb 5.
Published in final edited form as: Nat Struct Mol Biol. 2006 Sep 24;13(10):879–886. doi: 10.1038/nsmb1150

Figure 1.

Figure 1

Location of the Ksg-binding pocket in the ribosome. (a) Secondary structure of 16S rRNA, showing the resistance sites (large characters) and residues in contact with Ksg (small characters). Sites of altered reactivity toward chemical probes in the presence of Ksg are shown as filled circles (protections) or empty circles (enhancements). (b) The Ksg-binding pocket in the context of the 30S subunit, highlighting Ksg (cyan), the 790 loop (green), the 926 region (blue) and the DASL (red). Residues A794, G926, A1518 and A1519 are shown as sticks. (c) Close-up view of the Ksgbinding pocket of 30S-1 showing Ksg (cyan) docked into the positive electronic density (blue mesh). Also shown: negative electronic density (red), resistance sites (gold) and contact sites (gray). (d) Contact sites, color-coded as in c. (e) Location of Ksg relative to P-site tRNA and mRNA. Shown are Ksg (cyan), P-site mRNA (red), E-site mRNA (blue), anticodon stem-loop (green). mRNA residues are labeled with position relative to first base of P-site codon (+1). ASL and mRNA coordinates were extracted from the structure of the T. thermophilus 30S subunit (PDB entry 1FJG)6.