Figure 3. Details of fluoride ion binding site in the T. petrophila fluoride riboswitch in the ligand bound state.

a, An expanded stereo view highlighting the non-bridging phosphate oxygens directly coordinated to the three Mg²⁺ ions labeled M1, M2 and M3, that are in turn directly coordinated to the fluoride ion. In terms of nomenclature, the phosphate labeled pA6 corresponds to the G5pA6 step. Three of the phosphates are involved in bidentate coordination with the metals, while two are involved in mondentate coordination. b, The fluoride ion is positioned 0.49 Å above the plane formed by the three metal ions. c, A stereo view of the coordination geometries of fluoride ion with surrounding Mg²⁺ ions, and in turn of Mg²⁺ with surrounding non-bridging phosphate oxygens and waters. Metal coordination within square-planar positions are shown by dashed blue lines, while coordination in apical positions are shown by dashed red lines in panels a, c and d. d, These panels show the octahedral coordination geometries around Mg²⁺ ions M1, M2 and M3, together with coordination distances in Å.