Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 37

Table 2.2 Comparison between crystallographic and simulation data for selected
heavy-atom distances in the HHR active site with Mg 2þ initially placed at the bridging
position (B-site, Fig. 2.2 )

X-ray Simulation

2GOZ 2OEU RT-B ETS-B LTS-B

C1.1:O2P A9:O22P 4.33 4.28 3.36 (49) 4.00 (60) 4.01 (70)

Mg 2 þ G8:O2 0 3.04 3.14 3.97 (102) 2.24 (13) 3.21 (23)

Mg 2 þ C1.1:O5 0

3.84 4.01 4.22 (21) 3.68 (35) 2.09 (50)

G8:O2 0 C1.1:O5 0 3.19 3.51 4.29 (77) 4.41 (65) 2.91 (17)

C17:O2 0 C1.1:P 3.18 3.3 3.61 (23) 1.89 (12) 1.76 (40)

C17:O2 0

G12:N1 3.54 3.26 3.02 (27) 3.14 (28) 2.97 (13)

A9:N6 G12:N3 2.63 3.22 3.27 (58) 3.15 (21) 3.17 (21)

G12:O2 0 A9:N6 3.21 2.98 3.36 (86) 3.01 (18) 2.99 (16)

A9:N7 G12:N2 2.9 2.9 3.42 (93) 3.85 (44) 3.66 (33)

Average values are shown with standard deviations in the parentheses (divided by the decimal precision).
For simulation summary and abbreviations, see Table 2.1 .
2GOZ: The eHHR crystallographic structure at 2.2 ˚ resolution that was also used in this chapter as the
starting structure. 73 2OEU: The eHHR crystallographic structure at 2.0 ˚ resolution with resolved
Mn 2 þ sites and solvent. 74

Table 2.3 Comparison between crystallographic and simulation data for selected
heavy-atom distances in the HHR active site with Mg 2þ initially placed at the C-site
( Fig. 2.2 )

X-ray Simulation

2GOZ 2OEU RT-C dRT-C ETS-C ETS-C

C1.1:O2P A9:O22P 4.33 4.28 5.02 (97) 2.92 (26) 4.02 (6) 3.78 (27)

Mg 2 þ G8:O2 0

3.04 3.14 5.92 (28) 4.84 (36) 3.66 (61) 2.9 (85)

Mg 2 þ C1.1:O5 0 3.84 4.01 7.01 (79) 4.23 (41) 3.59 (16) 2.09 (6)

G8:O2 0 C1.1:O5 0 3.19 3.51 4.54 (59) 3.21 (35) 5.26 (72) 3.66 (73)

C17:O2 0

C1.1:P 3.18 3.3 3.55 (20) 3.57 (16) 1.86 (4) 1.76 (4)

C17:O2 0

G12:N1 3.54 3.26 4.92 (81) 2.99 (16) 2.95 (14) 3.66 (84)

A9:N6 G12:N3 2.63 3.22 3.11 (17) 3.12 (21) 3.14 (18) 3.14 (21)

G12:O2 0 A9:N6 3.21 2.98 3.07 (19) 3.36 (36) 3.03 (18) 3.09 (22)

A9:N7 G12:N2 2.9 2.9 3.00 (14) 3.07 (20) 3.60 (44) 3.06 (23)

Average values are shown with standard deviations in the parentheses (divided by the decimal precision).
For simulation summary and abbreviations, see Table 2.1 .
2GOZ: The eHHR crystallographic structure at 2.2 ˚ resolution that was also used in this chapter as
the starting structure. 73 2OEU: The eHHR crystallographic structure at 2.0 ˚ resolution with resolved