Fig. 5: The case of the FMN riboswitch.
From: Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN
A Key RNA binding site residues for the FMN ligand (PDB 2yie) and ribocil (PDB 5kx9) families. B Key RNA binding site residues for the DKM ligand (PDB 6bfb) and in the apo conformation (PDB 6wjr). C, D Cartoon representation of holo-like (C) and apo (D) starting structures used in the SHAMAN simulations of the FMN riboswitch. In the insets, the key binding site residues are overlayed with the probe densities (colors as in Tab. S7 and S8). E 2D structures of the probes that successfully identified the experimental binding sites in the FMN riboswitch. The brown and cyan dashed circles indicate the successful probes in the holo-like and apo simulations, respectively. F, G For the holo-like (F) and apo (G) simulations, the SHAMAPs with best overlap with FMN (left) and DKM (right) ligands, representing the two different binding modes of the FNM riboswitch.
