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. Author manuscript; available in PMC: 2015 Nov 13.
Published in final edited form as: Biochim Biophys Acta. 2014 Feb 28;1839(10):908–918. doi: 10.1016/j.bbagrm.2014.02.012

Fig. 4.

Fig. 4

Examples of ligand-binding pockets. RNA (grey) and ligands (hot pink) are shown in surface representation with heteroatoms depicted in the following colors: oxygen, red; nitrogen, blue; phosphorus, orange. All views are from the top in respect to the Fig. 3C,D views. (A), Tight lysine-bound pocket of the lysine riboswitch shows good shape complementarity with bound lysine [79]. A potassium cation (violet sphere) mediates interactions between the carboxylate of lysine and RNA. Nucleotides from the front are removed to visualize the pocket. (B) Semi-open pocket of the THF riboswitch bound to THF [90]. The pocket is located in the junctional region.