Fig. 6.

Structures of the TPP riboswitch bound by compounds identified in this study and by the native TPP ligand. Nucleotides in direct contact with the organic ligands are beige. Mg²⁺ and Mn²⁺ cations and water molecules are depicted as green, lavender, and red spheres, respectively; spheres do not represent physical sizes of ions and water molecules. Intermolecular hydrogen and metal ion coordination bonds are shown as gray and green dashed lines, respectively. Crystal structures of riboswitch bound by (A) compound 17, (B) TPP, and (C) compound 38. Arrow in B shows rotation of G72 in the 17-bound structure. (D) Relative positions of 38 and TPP ligands. (E) Model of Z1 bound to riboswitch. Arrow shows postulated displacement of Mn²⁺ atom (Mn2). (F) Surface view for model of Z1 bound to RNA. TPP (light green color and thin sticks) is shown as a reference; for clarity, a few nucleotides at the front of the structure were removed in this image. Py, pyrimidine; Tz, thiazole; PP, pyrophosphate moieties of TPP; Ox, quinoxaline; Pi, pyridine; Pip, piperazine of 38. TPP-bound structure is from 2GDI (28).