Table 1.
Summarya of Important Hydrogen Bonding Interactions (occupancies > 20%) Between Substrates and Functional Groups around Binding Pocket During the Production Phase of MD Simulations
| Residue | Functional Group | Substrate Atom | Distance (Å) (SDb) | Angle (°) (SDb) | Occupancy (%) |
|---|---|---|---|---|---|
| Substrate I | |||||
| Arg172 | N1-H2 | O4 | 2.785 (0.10) | 161.33 (9.04) | 99.72 |
| Tyr98 | O-H | O4 | 2.769 (0.15) | 158.21 (11.20) | 99.17 |
| Arg225 | N2-H1 | O4 | 2.887 (0.17) | 149.78 (12.31) | 97.50 |
| Arg225 | N2-H2 | O5 | 3.032 (0.21) | 144.04 (11.26) | 96.39 |
| Arg225 | N1-H2 | O5 | 2.892 (0.16) | 153.73 (10.79) | 95.56 |
| Arg225 | N3-H | O6 | 2.919 (0.17) | 152.15 (10.51) | 95.00 |
| Arg225 | N2-H1 | O6 | 3.043 (0.19) | 141.83 (9.49) | 93.33 |
| Arg227 | N2-H1 | O1 | 2.887 (0.17) | 145.58 (12.13) | 92.78 |
| Arg225 | N2-H2 | O1 | 3.000 (0.21) | 155.81 (10.35) | 89.72 |
| Ser171 | O-H | O1 | 2.764 (0.19) | 149.60 (13.42) | 88.06 |
| Arg25 | N2-H2 | O2 | 2.920 (0.15) | 154.23 (10.58) | 43.06 |
| Arg172 | N1-H1 | O1 | 3.177 (0.22) | 134.00 (8.99) | 40.00 |
| Arg25 | N1-H2 | O2 | 3.030 (0.20) | 145.46 (11.77) | 38.06 |
| Arg172 | N2-H2 | O4 | 3.265 (0.18) | 134.77 (6.90) | 28.06 |
| NADPH | C=O | N3-H18 | 3.030 (0.20) | 151.39 (11.93) | 21.11 |
| Substrate II | |||||
| Arg172 | N2-H2 | O6 | 2.822 (0.12) | 163.21 (8.99) | 100.00 |
| Arg172 | N1-H2 | O4 | 2.840 (0.13) | 162.98 (8.88) | 100.00 |
| Arg172 | N1-H1 | O1 | 2.841 (0.14) | 157.81 (10.95) | 80.56 |
| Arg172 | N2-H2 | O4 | 3.250 (0.17) | 135.78 (6.39) | 73.33 |
| Arg225 | N2-H2 | O1 | 2.922 (0.19) | 158.50 (12.83) | 70.00 |
| Arg225 | N2-H2 | O5 | 3.041 (0.23) | 147.24 (15.28) | 65.28 |
| Lys219 | N-H2 | O6 | 2.838 (0.12) | 160.43 (9.88) | 65.00 |
| Arg227 | N2-H2 | O5 | 2.895 (0.17) | 152.87 (12.60) | 63.61 |
| Arg225 | N2-H1 | O4 | 2.980 (0.20) | 155.82 (10.09) | 60.28 |
| Arg225 | N1-H2 | O5 | 2.911 (0.20) | 157.09 (12.87) | 59.17 |
| Arg227 | N1-H2 | O1 | 2.939 (0.19) | 156.60 (11.13) | 53.89 |
| Arg227 | N1-H2 | O5 | 3.001 (0.21) | 146.49 (11.54) | 38.33 |
| Arg227 | N2-H2 | O1 | 3.066 (0.20) | 142.22 (11.80) | 34.72 |
| NADPH | C=O | N2-H11 | 3.077 (0.20) | 141.87 (12.85) | 29.17 |
| Arg172 | N1-H2 | O6 | 3.354 (0.11) | 132.61 (5.88) | 21.94 |
| Lys219 | N-H3 | O6 | 2.847 (0.15) | 156.03 (10.96) | 21.39 |
| Arg18 | N1-H2 | O2 | 2.923 (0.16) | 148.16 (11.22) | 20.28 |
| Substrate III | |||||
| Arg172 | N1-H1 | O1 | 2.842 (0.13) | 157.52 (10.45) | 100.00 |
| Ser171 | O-H | O1 | 2.666 (0.12) | 163.99 (8.48) | 99.72 |
| NADPH | C=O | N2-H11 | 2.818 (0.11) | 159.67 (9.81) | 90.00 |
| Arg225 | N2-H1 | O4 | 2.904 (0.18) | 154.57 (12.38) | 70.00 |
| NADPH | C=O | N1-H2 | 3.109 (0.18) | 138.69 (12.06) | 52.78 |
| Arg172 | N1-H1 | O4 | 3.137 (0.20) | 131.08 (7.33) | 43.33 |
| Arg227 | N1-H1 | O4 | 2.853 (0.14) | 152.08 (9.59) | 34.72 |
| Substrate IV | |||||
| Arg172 | N1-H2 | O3 | 2.827 (0.11) | 154.80 (11.63) | 99.72 |
| Arg225 | N3-H | O3 | 2.887 (0.14) | 152.00 (9.39) | 99.17 |
| Arg172 | N2-H2 | O4 | 2.904 (0.16) | 160.33 (10.40) | 98.89 |
| Arg225 | N2-H1 | O3 | 2.890 (0.17) | 146.28 (9.60) | 96.67 |
| Arg225 | N2-H2 | O5 | 2.888 (0.18) | 152.59 (13.31) | 93.06 |
| Arg172 | N1-H2 | O4 | 3.212 (0.18) | 140.74 (8.45) | 81.39 |
| Arg225 | N1-H2 | O5 | 3.094 (0.25) | 140.55 (11.28) | 62.50 |
| Arg225 | N1-H2 | O6 | 2.955 (0.19) | 160.62 (9.83) | 44.72 |
| Arg227 | N1-H2 | O6 | 2.982 (0.21) | 149.06 (12.60) | 43.89 |
| Ser171 | O-H | O5 | 2.693 (0.13) | 164.38 (8.57) | 39.72 |
| Arg227 | N2-H2 | O6 | 2.961 (0.22) | 151.93 (12.74) | 21.39 |
| Substrate V | |||||
| Arg227 | N2-H2 | O5 | 2.882 (0.15) | 160.44 (9.75) | 98.89 |
| Arg225 | N1-H2 | O1 | 2.876 (0.16) | 153.18 (11.75) | 96.94 |
| Arg225 | N2-H2 | O1 | 3.011 (0.22) | 141.82 (11.37) | 92.50 |
| Arg227 | N1-H2 | O1 | 2.947 (0.19) | 151.41 (12.45) | 90.00 |
| Arg225 | N2-H2 | O5 | 2.935 (0.18) | 158.80 (10.22) | 88.33 |
| Arg172 | N1-H1 | O5 | 3.030 (0.18) | 146.31 (11.00) | 80.56 |
| Arg225 | N2-H1 | O4 | 2.918 (0.20) | 151.73 (13.88) | 80.56 |
| Arg172 | N1-H2 | O6 | 2.932 (0.22) | 153.12 (12.58) | 75.00 |
| Arg225 | N2-H1 | O6 | 2.930 (0.19) | 149.78 (13.85) | 69.72 |
| Arg172 | N1-H2 | O4 | 2.940 (0.23) | 153.01 (12.44) | 68.06 |
| Arg227 | N1-H2 | O5 | 3.154 (0.21) | 138.93 (8.13) | 63.89 |
| Tyr98 | O-H | O6 | 2.760 (0.17) | 149.52 (12.90) | 50.56 |
| Tyr98 | O-H | O4 | 2.766 (0.16) | 149.20 (11.90) | 41.39 |
| Arg227 | N2-H2 | O1 | 3.243 (0.19) | 135.22 (9.41) | 40.28 |
| Ser171 | O-H | O5 | 2.904 (0.29) | 151.45 (14.19) | 26.11 |
| Arg225 | N3-H | O4 | 3.089 (0.23) | 146.14 (10.08) | 25.28 |
| Arg225 | N3-H | O6 | 3.097 (0.22) | 143.63 (9.58) | 22.50 |
a
The order is ranked by the occupancies (from largest to smallest).
b
Standard Deviation.