Figure 4.

The initial arrangement (the first NMR frame, top left) of the U1/G2/C3/Phe126 hydrophobic pocket and the three alternative conformations seen in the simulations during time periods where the C3 nucleotide was stably bound. The Sim1 conformation was the most common while the others were less frequent. The H-bonds are indicated by dotted lines between heavy atoms. The Table summarizes the stacking interactions, H-bonds, and the number of satisfied protein–RNA intermolecular NOE distances in the specific conformations. PDB files of representative structures can be found in Supporting Information.