Table 2.
Orientation of water chains in the nonpolar cavity of the enzyme in different redox states
| Redox state | PUMP* | CHEM* |
| PM | 16,963 (28) | 2,520 (4) |
| PM' | 29,488 (46) | 143 (0.2)/3.8† |
| PR | 4,826 (7) | 7,418 (11) |
| F | 764 (2.5) | 0 (0) |
| F' | 10,756 (36) | 3 (0.01)/5.6† |
| FR | 4,261 (14) | 3,343 (11) |
| FH' | 16,304 (24) | 279 (0.4)/3.4† |
| FH,R | 142 (0.2) | 12,219 (18) |
| F'C | 4,356 (14) | 5,868 (19)/1.0† |
| F' ‡ | 12,160 (41) | 0 (0) |
PUMP denotes a complete water wire from Glu242 to the Dprp of the high-spin heme, and CHEM denotes a corresponding water wire to the binuclear site (Fig. 2), based on the hydrogen bonding criteria described in Materials and Methods. The total number of frames in each configuration is given, along with the percentage of the observed water chain out of all frames, in parentheses.
Energy cost [being described as –kB T ln P(CHEM) in units of kcal/mol] associated with the formation of the CHEM configuration in the states when heme a is reduced.
Data based on charge parameterization used in Yang and Cui (ref. 24, and references therein) but with the structure of the F' state as described in the current work.