Fig. 8.
The internal loop structure of the active stem-loop I is a recurring tertiary interaction motif. (a) Sequence and secondary structure of the pattern searched by MC-Search and of helix 25 of 23S rRNA of H. marismortui (1). (b) A superposition between helix 25 (PDB code 1JJ2; 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 (1.70 Å). Also shown are residues in helix 41 of 23S rRNA, which form a tertiary interaction with helix 25. (c) Summary of the base-pairing and stacking interactions in helices 41 and 25 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 tertiary contacts (red dashed lines). The two adenines A565 and A566 participate in A-minor motifs (green dashed lines).1. Klein, D. J., Schmeing, T. M., Moore, P. B. & Steitz, T. A. (2001) EMBO J. 20, 4214–4221.