Table 3.
Dynamic features of R185 observed in the REMD trajectories of P450eryF
| Traj #* | R185
χ†
|
Residues H-bonding to
R185‡
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| χ1 | χ2 | χ3 | 74 | 75 | 76 | 77 | 173 | 174 | 175 | 176 | 177 | 178 | 182 | |
| Crystal | t | t | t | X | X | X | X | |||||||
| 1 | t | t | t | b | F | b | f | f | b | B | ||||
| 2 | g− | t | t | B | b | f | B | B | f | f | f | |||
| 3 | t | t | g+ | B | f | b | f | b | f | B | ||||
| 4 | g+ | t | g+ | B | X | F | B | B | f | f | F | |||
| 5 | g+ | t | g+ | B | F | b | F | f | B | B | f | f | F | |
Trajectories are numbered as in Table 2.
The dihedral angles of the R185 sidechain are defined as in ref. 28, and for the REMD trajectories are those found immediately after the expulsion event. With the exception of traj #1, the conformation of R185 in all REMD trajectories is more solvent exposed after ligand exit.
H-bond formation to R185 during the simulations is represented as: X, crystallographic; b, crystallographic H-bond breaks and reforms several times during the simulation; B, crystallographic H-bond is broken for most of the simulation; f, noncrystal H-bond transiently forms and breaks several times during the simulation; F, noncrystal H-bond forms for an extended period of simulation.