Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 59

Figure 2.9 The 3D density contour maps (white) of Na þ ion distributions derived from
the RT-Na (upper panels) and dRT-Na simulations (low panels) at different isodensity
contour levels (left panels: 0.1; right panels: 1.0). The HHR is shown in dark gray. The
figure shows that, although the Na þ ions distribute around the RNA phosphate back-
bone (left panels), the HHR folds to form a local electronegative recruiting pocket that
attracts a highly condensed distribution of the Na þ ions (left panels) both in the reactant
state and the deprotonated activated precursor state (deprotonated C17:O2 0 )
simulations.
4.2. Discussion
Our simulations suggest that in order to maintain the active in-line confor-
mation, the highly negative charged environment of the active site needs to
be balanced by a threshold cation occupancy. This can be accommodated in
the reactant state by either a single Mg 2 þ ion, or one to two Na þ ions. In the