Figure 2.

Ribbon diagrams of the preQ₁-free and preQ₁-bound states of the Tte preQ₁-I riboswitch and select Mn²⁺ binding sites. (A) Ribbon diagram depicting the H-type pseudoknot fold of the preQ₁-I riboswitch based on the preQ₁-free Tte crystal structure of this investigation. Six Mn²⁺ binding sites (maroon spheres) are labeled. Structural elements are colored and labeled as in Figure 1. (B) Ribbon diagram of the preQ₁-bound co-crystal structure from this investigation; preQ₁ is depicted as a CPK model (green); the site Ib ion is observed only in the preQ₁-bound state. (C) Ball-and-stick and ribbon diagram depicting the site II Mn²⁺ ion, which binds similarly in the preQ₁-free and bound-state structures. Water molecules are denoted by wat. (D) Diagram depicting the site III Mn²⁺ ion, which is compatible with the preQ₁-free conformation. (E) Diagram depicting the site IV Mn²⁺ ion, which is compatible with both free and bound-state conformations.