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

Figure 6. Sequence alignment and annotated tertiary motifs in lysine riboswitches.

Figure 6

(A) Sequence alignment of lysine riboswitches where gray shaded columns indicate the highly conserved nucleotide positions. Other color shaded columns indicate regions involved in tertiary interactions (brown: A-minor, yellow: loop-receptor interaction and green: kissing-loop complex). For clarity, not all tertiary motif positions are numbered. Base-triple positions that are not conserved are in cyan shaded columns. (B) Tertiary structure of T. maritima lysine riboswitch [23] (PDB ID = 3dil). The ligand is represented as spheres and the highly conserved nucleotides are in wire representation. Base triple (A127-A23-G69) and base quadruple (G11-G163-G141-A162) interactions are presented in blue and red respectively.