Fig. 5.

The internal loop structure of the active stem-loop I is a tertiary interaction motif (a) Sequence and secondary structure of the pattern searched by mc-search and of helix 44 of 16S rRNA of T. thermophilus (40) (b) A superposition between helix 44 (PDB ID code 1FJG; pastel colors) and the minimized average structure of SL1′ (darker colors) was obtained by minimizing the rmsd for heavy atoms of the five residues in the internal loop (1.40 Å). Also shown are residues in helix 13 of 16S rRNA, which form a tertiary interaction with helix 44 (c) Summary of the base-pairing and stacking interactions in helices 13 and 44 and of tertiary contacts between them. Solid and dashed black lines indicate base pairs with two hydrogen bonds (either Watson–Crick or sheared G-A) and one hydrogen bond, respectively. Black rectangles indicate base stacking. Red spheres indicate riboses involved in ribose–ribose contacts (red dashed lines). The two adenines A1433 and A1434 participate in A-minor motifs (green dashed lines).