Fig 3. Distributions and effects of Mg²⁺.

(A) Density contours of Mg²⁺ ions in the Q₁-bound complex, shown as wireframe. Three Mn²⁺ ions in PDB entry 6VUI are shown as ochre spheres; the corresponding Mg²⁺ sites are labeled as M1, M2, and M3. Phosphate groups in G4 and A13 are shown in stick representation, to highlight the bridging role of M2. (B) Two views showing the coordination of the Mg²⁺ ion at the M2 site. Top: coordination of Mg²⁺ by six water molecules and the latter’s hydrogen bonding with the G3 and G4 nucleobases and A14 phosphate. Bottom: two distances, d_4-13 (between G4 O6 and A13 OP1) and d_14-16 (between A14 P and C16 N4), introduced to characterize the effects of the Mg²⁺ ion. (C) Probability densities of d_4-13 and d_14-16, in cMD simulations with and without Mg²⁺ ions. (D) Effect of Mg²⁺ ions on the separation of the L2 loop from the S1 helix in the Q₁-bound form. Two representative structures are superimposed, with the aptamer in the presence of Mg²⁺ shown in the same multi-color scheme as in Fig 1A and the aptamer in the absence of Mg²⁺ shown in a uniform cyan color. In the bottom view, the C15 nucleotides in the two structures are shown in a stick representation.