Variations of the structure of the A-wedge motif. (A) The nucleotide sequences of two modifications of the A-wedge motif observed in motifs L639 from the H. marismortui 23S rRNA (L639-Hm) (Ban et al. 2000) and S62 from the E. coli 16S rRNA (Schuwirth et al. 2005). Each secondary structure is drawn using the same AGPM template as in Figure 2A. In each case, the nucleotide numbering is taken from the original publication of the corresponding structure. (B) Stereo view of the tertiary structure of the “half-wedge” observed in AGPM S62. For nucleotide −3P, only the ribose and backbone are shown. (White) Base pairs at the −1-level; (gray) nucleotides −2P and −2R; (black) nucleotides −3P, −2Q, and −2S. The positions of nucleotides −2P, −3P, and −2Q in S62 are superposable with those in the standard A-wedge arrangement with RMSD 0.59 Å (data not shown). Unlike in the standard A-wedge structure, nucleotide −2S does not stack to −2Q, but instead, forms a WC base pair with nucleotide −2R. A color version is provided in Supplemental Figure 3.
