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. 2012 Feb;18(2):300–307. doi: 10.1261/rna.028779.111

FIGURE 5.

FIGURE 5.

Effects of ligand binding to SAM-II riboswitch on its EP. Probability distributions of the distances between the key base pairs in the expression platform along the P2a/b helix, i.e., N3 of U20 and N1 of A46 (A), N6 of A19 and N3 of A47 (B), and O2 of U18 and N6 of A48 (C) when the SAM-II riboswitch is unbound (black) or bound either to (S,S)-SAM (blue), (R,S)-SAM (green), or SAH (red). The distributions of the effective curvature of the expression platform are shown in D for all four cases: the unbound riboswitch (black) and that bound to (S,S)-SAM (blue), (R,S)-SAM (green), or SAH (red). (Inset to D) Ensemble of structures of the free (left inset) and the SAM-bound (right inset) SAM-II with curvatures corresponding to the peak of the respective distributions.