Table 3. Hydrogen bonds existing in Loop 2 (residues from 214 to 229) of wild-type NDM-1 and Y229W mutant, and their occupancies during the last 4 ns of MD simulations.
NDM-1 | Y229W mutant | ||||
Donor | Acceptor | Occupancy (%) | Donor | Acceptor | Occupancy (%) |
K214@ N | D212@OD1 | 84.14 | K214@ N | D212@OD1 | 88.96 |
H261@ NE2 | A215@O | 90.19 | H261@ NE2 | A215@O | 98.06 |
A215@ N | D212@O | 99.55 | A215@ N | D212@O | 98.00 |
A224@ N | N220@O | 99.76 | —— | —— | —— |
D223@ N | N220@O | 98.04 | —— | —— | —— |
G222@ N | N220@OD1 | 85.64 | —— | —— | —— |
—— | —— | —— | W229@ N | D225@O | 55.38 |
—— | —— | —— | H228@ N | D225@O | 53.72 |
E227@ N | D225@OD1 | 99.10 | —— | —— | —— |
H228@ N | D225@OD1 | 99.43 | —— | —— | —— |
D225@ N | G188@O | 99.45 | —— | —— | —— |
—— | —— | —— | A230@ N | T226@O | 85.96 |
—— | —— | —— | T226@ OG1 | L269@O | 57.93 |
S232@ N | H228@O | 96.63 | S232@ N | H228@O | 98.58 |
A231@ N | H228@O | 60.30 | —— | —— | —— |
Y229@ OH | L209@O | 99.83 | W229@ NE1 | L209@O | 98.75 |
A233@ N | Y229@O | 93.83 | A233@ N | W229@O | 96.86 |
Only H-bonds with occupancies >50% are shown.
—— Not observed.