Figure 2.

Schematic illustration of the active site of the genomic HDV ribozyme and the reaction coordinates included in the string calculations. The QM region for the QM/MM calculations consists of the 87 atoms shown in red, including the U-1 base and sugar, the G1 phosphate (the scissile phosphate) and sugar, the protonated C75 base, the U23 phosphate, the sugar of C22, the active site Mg²⁺ ion, and the three crystallographic waters coordinating to the Mg²⁺ ion. The reaction coordinates included in the string calculations are indicated by the blue double-headed arrows. In total, 12 active site distances were considered, although r1, r2, r3, and r4 were found to be the most important. The reaction paths are typically projected onto collective coordinates, namely, the difference of r1 and r2 (r1 – r2) and the difference of r3 and r4 (r3 – r4).