Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 52

175

150

125

RT-C-Mg

100

175

150

125

RT-B-Mg

100

175

150

125

RT-Na

100

175

150

125

dRT-Mg

100

175

150

125

dRT-Na

100

3 3.2 3.4 3.6 3.8 4 4.2 4.4

R(C17:O 2 -C1.1:P) in Å

Figure 2.7 Plot of the C17:O2 0 P d C1.1:O5 0 angle versus C17:O2 0 d P distance for the
approach of the 2 0 -hydroxyl of residue C17 to the phosphate of residue C1.1 for the reac-
tant state (RT) and the activated state (dRT) simulations. C-Mg indicates that the Mg 2þ
was initially placed at the C-site position, while B-Mg means the Mg 2þ ion was initially
placed in the B-site position. Data obtained from the last 250 ns of the simulations are
shown with a frequency of 50 ps and points are colored according to the clustering
results and Table 2.6 : cluster A (light gray) and cluster B (dark gray). The light gray lines
at 3.25 Å and 150 degrees indicate the near in-line attack conformation (NAC) region
defined by Torres and Bruice. 135