Ion distribution determination

The 3D density contour maps for the Na+ ion distribution determined over the last 250 ns of simulation (Figure 14-8) show that the overall highest probability Na+ occupation sites were concentrated in the active site for both the reactant and activated precursor. This suggests that the HHR folds to form a strong local electronegative pocket that is able to attract and bind Mg2+ if present in solution, or recruit a high local concentrations of Na+ ions in the absence of Mg2+. 

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