Table 5. Root-Mean-Square Fluctuations (angstroms) of Cα Atoms for the Catalytic Base Loop Residues 38–42 Obtained from MD Simulationsa.
| enzyme | Asp38(Glu) | Pro39(Gly) | Val40(Gly) | Gly41 | Ser42(Gly) |
|---|---|---|---|---|---|
| WT | 0.48 (0.02) | 0.58 (0.04) | 0.54 (0.05) | 1.00 (0.08) | 0.72 (0.02) |
| A114G | 0.50 (0.04) | 0.60 (0.04) | 0.55 (0.03) | 1.01 (0.03) | 0.76 (0.02) |
| P39G | 0.66 (0.09) | 1.00 (0.24) | 1.60 (0.13) | 2.85 (0.35) | 2.04 (0.24) |
| P39G/V40G/S42G | 0.53 (0.12) | 0.85 (0.30) | 1.20 (0.52) | 1.72 (0.70) | 1.59 (0.59) |
| S42G | 0.48 (0.02) | 0.55 (0.02) | 0.53 (0.03) | 0.90 (0.04) | 1.26 (0.43) |
| V40G/S42G | 0.51 (0.03) | 0.75 (0.10) | 0.97 (0.23) | 1.28 (0.20) | 1.51 (0.28) |
| D38E | 0.69 (0.18) | 0.75 (0.25) | 0.62 (0.11) | 0.98 (0.11) | 0.90 (0.10) |
| D38E/A114G | 0.53 (0.08) | 0.67 (0.08) | 0.66 (0.07) | 1.18 (0.09) | 0.85 (0.10) |
| D38E/P39G | 0.49 (0.03) | 0.79 (0.22) | 0.90 (0.14) | 1.61 (0.21) | 1.28 (0.10) |
| D38E/P39G/V40G/S42G | 0.68 (0.05) | 1.04 (0.23) | 1.88 (0.31) | 2.33 (0.46) | 1.94 (0.18) |
a
Results obtained by averaging over two 20 ns MD trajectories and two active sites. Standard deviations among the four data sets are shown in parentheses.