Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 55

Table 2.7 Characterization of the Mg 2þ coordination in the active site
R C17:O2 0 G8:O2 0

u O d O A9:O2P C1.1:O2P G10:N7

RT-C-Mg 4.01 (34) 126.5 (119) 4.14 (49) 2.01 (4) 4.40 (30) 6.04 (90) 5.76 (46) 4.19 (31)

RT-B-Mg 3.28 (12) 151.2 (79) 2.95 (13) 2.02 (5) 2.04 (5) 4.25 (24) 4.57 (30) 4.38 (25)
dRT-Mg 3.64 (17) 155.0 (80) 2.94 (13) 2.01 (4) 2.03 (5) 3.76 (17) 4.62 (62) 5.05 (26)
Analysis was performed over the last 250 ns (10 ps sampling frequency). Distances and angles are in ˚ and degrees, respectively. Standard deviations (SDs) are listed in
parentheses divided by the decimal precision of the average (e.g., if the average is reported to two digits of decimal precision, the SD is divided by 0.01). R is the in-line
attack distance (C17:O2 0 to C1.1:P); is the in-line attack angle (between C17:O2 0 , C1.1:P, and C1.1:O5 0 ); “O d O” is the distance between A9:O2P and C1.1:O2P; all

others are distance between the Mg 2 þ and the indicated ligand site.

y