Fig 5. Loosening in the back of the binding pocket when bound with synthetic ligands, in cMD simulations with Mg²⁺.

(A)-(C) Density contours of ligands, shown as wireframe in reference to a representative Q₁-bound structure, with the six pocket-lining nucleotides displayed in stick representation. Panel (A) shows contours in red for Q₁ and in green for Q₀; panel (B) shows contours in red for L₁ and in green for L₂; and panel (C) shows contours in red for L_3m and in green for L_3M. The L_3m and L_3M contours were calculated only from snapshots where hydrogen bonding with A29 or U6 was present. (D)-(F) Representative conformations of the Q₁-, L₁-, and L_3m-bound forms, respectively. Ligands are shown in both stick representation and as dot surface. The C1’ atoms of C15 and C30 are connected to define the distance d_15-30 and to illustrate the back door. (G) The probability densities of d_15-30 in the apo form and the five liganded forms. (H) Two views into Q₁ in the binding pocket. The aptamer is shown as gray surface while the ligand is shown as green spheres. Left: front view showing Q₁ exposure; right: back view showing buried Q₁. (I) Corresponding presentation for L₁, except that this ligand is exposed both on the front and on the back.