TABLE II.
Hydrogen Bond Distances, Ligand RMS Values, and Simulation Parameters for Three Treatments of Solvation and Electrostatics for the Complex with 1†
| Residue | Protein atom | Carbohydrate atom | X-raya | Droplet | PBC | PBC PME |
|---|---|---|---|---|---|---|
| His-44 | Nε | Gal-O4 | 2.8 | 3.0 (0.2)b | 3.0 (0.2) | 3.4 (0.4) |
| Asn-46 | Oδ1 | Gal-O4 | 3.4 | 3.4 (0.3) | 3.4 (0.3) | 3.4 (0.3) |
| Arg-48 | Nη2 | Gal-O4 | 3.0 | 2.9 (0.2) | 2.9 (0.2) | 3.0 (0.2) |
| Arg-48 | Nη2 | Gal-O4 | 3.0 | 2.9 (0.2) | 2.9 (0.1) | 3.0 (0.2) |
| Asn-61 | Nδ2 | Gal-O6 | 2.7 | 3.0 (0.2) | 2.9 (0.1) | 3.0 (0.2) |
| Glu-71 | Oε1 | Gal-O6 | 4.7 | 4.3 (0.6) | 3.8 (0.9) | 4.6 (0.2) |
| Glu-71 | Oε2 | Gal-O6 | 2.8 | 2.9 (0.6) | 3.5 (0.9) | 2.7 (0.1) |
| Arg-48 | Nη1 | GlcNAc-O3 | 2.8 | 2.9 (0.1) | 2.9 (0.1) | 2.8 (0.1) |
| Arg-48 | Nη2 | GlcNAc-O3 | 3.2 | 3.3 (0.3) | 3.4 (0.3) | 3.3 (0.2) |
| Arg-48 | Nη1 | GlcNAc-O4 | 4.2 | 4.1 (0.3) | 4.1 (0.3) | 4.3 (0.3) |
| Arg-48 | Nη2 | GlcNAc-O4 | 3.6 | 3.6 (0.3) | 3.5 (0.2) | 3.5 (0.3) |
| Glu-71 | Oε1 | GlcNAc-N | 4.0 | 3.8 (0.5) | 4.0 (0.6) | 3.5 (0.2) |
| Glu-71 | Oε1 | GlcNAc-O3 | 3.3 | 2.9 (0.3) | 2.9 (0.4) | 3.0 (0.2) |
| Glu-71 | Oε2 | GlcNAc-O3 | 2.4 | 3.2 (0.5) | 3.0 (0.4) | 2.8 (0.2) |
| Arg-73 | Nη1 | GlcNAc-C=O | 4.5 | 4.1 (0.6) | 4.3 (0.5) | 4.5 (0.6) |
| Arg-73 | Nη2 | GlcNAc-C=O | 3.3 | 4.5 (0.4) | 4.5 (0.4) | 4.6 (0.4) |
| Arg-73 | Nη1 | GlcNAc-O3 | 4.7 | 4.1 (0.5) | 4.5 (0.4) | 4.6 (0.4) |
| Arg-73 | Nη2 | GlcNAc-O3 | 3.3 | 3.1 (0.3) | 3.3 (0.3) | 3.4 (0.4) |
| Binding site RMSD | ||||||
| All atoms | 1.1 (0.4) | 1.0 (0.1) | 1.2 (0.2) | |||
| Backbone only | 0.7 (0.3) | 0.7 (0.1) | 0.9 (0.2) | |||
| LacNAc ring atoms only | 0.9 (0.3) | 0.7 (0.2) | 1.1 (0.4) | |||
| No. of particles | 7278 | 16056 | 16056 | |||
| Simulation time (h) | 168 | 436 | 604 | |||
†
Distances are in Ångstroms, and root-mean-squared deviation (Å) in the nonhydrogen atomic positions, relative to the X-ray structure.
a
Liao et al.15
b
Standard deviations in parentheses.