FIGURE 2.

Importance for TPP binding of structural features of the thi-box riboswitch. (A) Detail of the TPP binding pocket, with magnesium ion-dependent recognition of the pyrophosphate binding (left) and recognition of the aminopyrimidine by base pairing with G40 and stacking interactions. (Dashed lines) Hydrogen bonds, (solid lines) inner-sphere coordination. (B) P3–L5 interactions. (C) EMSA analysis shows that the mutation C77U is permissive for binding, whereas mutations A84U and G40U abolish binding (D). (E,F) EMSA analysis of mutants in positions 69 and 70 shows that only A69C, A69U, and A70G are permissive of binding. RNA concentration was 40 μM in C–F.