Molecular mechanism for preQ₁-II riboswitch function revealed by molecular dynamics

Distance between atoms in P3 nucleotides. The left panel corresponds to ligand-bound simulations and the right panel corresponds to the apo simulations. Four distances are color annotated and these distances each correspond to a base pair, as shown in the key. In many simulations, the plot of the N3 of U36 to N1 of A75 distance (green) is obscured by the N3 of U39 to N1 of A72 distance (purple), and is therefore not visible.