Table 1. Experimental and Calculated Fine Structure Parameters, D and E, of the N-Terminal and C-Terminal Mn(II) Binding Sites in WT OxDC and the W132F OxDC Variant.
| site I |
site
II |
||||
|---|---|---|---|---|---|
| enzyme (active site) | type (pH) | D (MHz) | E/D | |D| (MHz) | E/D |
| WT OxDC | experimental (8.5) | –1350 | 0.15a | 10430 | 0.20a |
| WT OxDC (Tabares et al.)12b | Experimental (8.8) | –1110 | 0.27 | 10730 | 0.16 |
| WT OxDC (N-terminal) | DFT/MM-optimized | –1170 | 0.11 | g | |
| WT OxDC (C-terminal)b | DFT/MM-optimized | 4110h | 0.22 | ||
| WT OxDC (C-terminal)c | DFT/MM-optimized | 4560h | 0.14 | ||
| WT OxDC (C-terminal)d | DFT/MM-optimized | 7130h | 0.13 | ||
| W132F | experimental (8.5) | –1950 | 0.21a | 10430 | 0.20 |
| W132F (N-terminal)e | DFT/MM-optimized | –2100 | 0.23 | ||
| W132F (N-terminal)f | DFT/MM-optimized | –1350 | 0.10 | ||
The error for E/D values obtained in the present study is very large due to the broad distribution of E values that had to be assumed in the simulations. These values are obtained from the center of a broad Gaussian distribution of E (see text for more details).
Cluster model containing water as the fifth ligand (Figure 7b).
Cluster model containing hydroxide as the fifth ligand (Figure 7c).
Cluster model containing hydroxide as the fifth ligand with a hydrogen bond to a solvent water (Figure 7d).
Initial structure for QM/MM optimization based on the X-ray crystal structure of Co(II)-containing W132F OxDC variant.
Initial structure for QM/MM optimization from in silico modification of the X-ray crystal structure of WT OxDC (1UW8).
Not applicable.
In the text, we report either the positive or the negative D value as obtained by calculation. In this table, however, we give only absolute values for D in the case of the C-terminal site because the sign of this parameter could not be experimentally determined.