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. 2013 Sep 5;8(9):e73984. doi: 10.1371/journal.pone.0073984

Figure 5. Sequence alignment and annotated tertiary motifs in preQ1 riboswitches.

Figure 5

(A) Sequence alignment of preQ1 riboswitches where gray shaded columns indicate the highly conserved nucleotide positions. Brown shaded columns indicate regions involved in the pseudo-cis ribose-zipper interaction. For clarity, not all tertiary motif positions are numbered. Base-triple positions that are not conserved are in cyan shaded columns. (B) Structural superposition between B. subtilis preQ1 riboswitch [22] (PDB ID = 3fu2/white backbone) and T. tengcongensis preQ1 riboswitch [42] (PDB ID = 3gca/dim gray backbone). The ligand is represented as spheres and the highly conserved nucleotides are in wire representation. Magnifications of the superposed triples using the numbering for 3fu2 are presented in blue (3fu2), cyan (3gca), red (3fu2) and magenta (3gca).