Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 58

1 2 3 4 5 6

1 2 3 4 5 6 1 2 3 4 5 6

6 6 6

5 5 5

4 4

4

3 3 3

2 2 2

dRT, no Mg, NotInLine dRT, no Mg, NotInLine dRT, no Mg, NotInLine

6 6 6

5 5 5

4 4 4

3 3 3

2

2 2

dRT, no Mg, InLine dRT, no Mg, InLine dRT, no Mg, InLine

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6

r (C1.1:O2P, Na) r (G8:O2 , Na) r (A9:O2P, Na)

Figure 2.8 Two-dimensional radial distribution function of Na þ ions in the active site for the activated precursor simulation without Mg 2þ
present in the active site (dRT-Na). The lower panels show results for cluster A that contains population members that are in active in-line
conformations, and the upper panels show results for cluster B that are not in-line (see Table 2.6 ). The axes are the distances (in Å) to different