Summary of simulations using secondary structure diagrams showing mapped long-range interactions. The top left structure is the crystal structure used as the starting conformation for all simulations. All four ligand-bound simulations converged to a common structure shown in the top right corner. Three of the apo simulations showed the same altered structure of the binding pocket (apo simulations 2, 3, and 4). This binding pocket includes nucleotides C30, U31, U32, U41, and A70. Apo simulation 1, however, has G76 and U34 stacked at the end of P3. The noncanonical pairs are annotated according to the standard Leontis–Westhof classification (Leontis et al. 2002; Zirbel et al. 2009). The SD sequence is highlighted in yellow. The base triple interactions that are present in ligand-bound simulations are absent in the apo simulations.
