Figure 2. The binding pocket of the PRPP riboswitch.
(A) Crystal structure of the ligand-binding site in chain A. Relative to Figure 1, the structure is rotated 180° about the y axis. PRPP is depicted as sticks and colored by element with purple carbons. Nucleotides are depicted as blue sticks. Metal ions are depicted as gray spheres. Individual nucleotides and metals are labeled. An FO–FC map contoured at 2.5 σ is shown as a gray mesh. The map was calculated using an otherwise complete model lacking PRPP, M1, and M2. (B) Ligand interaction map. The map is colored essentially as in A. All RNA and metal contacts to PRPP are shown. Dashed black lines indicate hydrogen bonds. Solid black lines indicate coordination to a metal ion. Brackets indicate interactions shown in individual panels of Figure 3.