Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 38

Figure 2.3 The Mg 2þ positions from snapshots of simulations with Mg 2þ initially placed
at the C-site position. Snapshots shown are for the initial C-site position (upper
left), the reactant state with C17:O2 0 protonated (upper right), the reactant state with
C17:O2 0 deprotonated (lower left), and the ETS mimic (lower right). The Mg 2þ position
in the LTS mimic is similar to the ETS mimic (not shown). The Mg 2þ ionmigrates from the
C-site to the position bridging the A9 and scissile phosphates (i.e., directly coordinated
with the A9:O2P and C1.1:O2P) in the transition state mimic simulations and in the reac-
tant state simulation with Mg 2þ initially placed at the C-site position and with C17:O2 0
deprotonated, but not in the reactant state simulation with C17:O2 0 protonated. The
distances shown are distances to Mg 2þ from A9:O2P, C1.1:O2P, and G10.1:N7.

and ETS-C) and in the reactant state simulation where the nucleophilic O2 0
has been deprotonated (dRT-C). However, in the parent reactant state sys-
tem (RT-C), where C17:O2 0 is protonated, the divalent metal ion stays in
the C-site in the course of the 12 ns MD simulation. The Mg 2 þ ion directly
coordinates to A9:O2P with a distance less than 2.5 ˚ for all simulations

(data not shown).

2.4.2 Mg 2þ binding and migration in the reactant state
In the reactant simulations with Mg 2 þ at the bridging position (RT-B), the
Mg 2 þ coordination between the C1.1 and A9 phosphate oxygens fluctuates
between axial-axial and axial-equatorial modes, resulting in a shorter