Table 1.
Comparison of characteristic catalytic inter-residue distances from available X-ray structures and calculated averages ± S.D. from MD simulations of OTUB1 and OTUB2 in Å
| Protein | Protein conformation | Catalytic site protonation state | His-Cys | Asp-His | His (N-CA-CB-CG) dihedral angle |
|---|---|---|---|---|---|
| Å | Å | ° | |||
| OTUB1 | Ub-bound | 4DDG | 3.5 | 3.3 | 165 |
| O1U1C | Charged | 3.3 ± 0.2 | 2.7 ± 0.1 | 173 ± 05/−175 ± 04 | |
| O1U1N | Neutral | 4.7 ± 1.5 | 4.6 ± 2.1 | 170 ± 17/−147 ± 45 | |
| Ub-free | 2ZFY | 5.5 | 6.7 | −65 | |
| O1U0C | Charged | 5.8 ± 1.8 | 4.8 ± 1.4 | 084 ± 52/−156 ± 41 | |
| O1U0N | Neutral | 6.4 ± 0.9 | 7.0 ± 1.2 | 145 ± 45/-067 ± 19 | |
| OTUB2 | Ub-bound | 4FJV | 4.0 | 2.9 | −179 |
| O2U1C | Charged | 5.9 ± 0.7 | 7.5 ± 1.8 | 074 ± 44/−059 ± 23 | |
| O2U1N | Neutral | 5.4 ± 1.2 | 6.5 ± 1.7 | 126 ± 62/−079 ± 46 | |
| Ub-free | 1TFF | 4.0 | 2.9 | −176 | |
| O2U0C | Charged | 5.5 ± 0.9 | 4.7 ± 1.9 | 149 ± 44/−138 ± 52 | |
| O2U0N | Neutral | 3.9 ± 0.8 | 4.5 ± 1.8 | 174 ± 05/−150 ± 44 |