Table 1. Minimum Distance between SILCS Pharmacophore-Identified Mg2+ Binding Sites and Experimentally Assigned Mg2+ Sites, and the Atomic GFE Scores for the Experimental Mg2+ Sitesa.
| system/site | minimum distance (Å) | atomic GFE (kcal mol–1) |
|---|---|---|
| Beet Western Yellow Virus (BWYV) Pseudoknot | ||
| Mg-29 | 2.01 | –4.47 |
| Mg-34 | 6.95 | +1.64 |
| Mg-38 | 2.82 | –1.58 |
| Mg-45 | 2.25 | –2.19 |
| Mg-52 | 2.58 | –1.86 |
| Mg-59 | 3.34 | +1.64 |
| Varkud Satellite (VS) Ribozyme SLVI | ||
| Mg-101 | 2.34 | –0.16 |
| Mg-102 | 4.18 | –0.88 |
| Mg-103 | 3.52 | –3.03 |
| Mg-104 | 0.91 | –3.44 |
| Mg-105 | 2.94 | –1.47 |
| 23S rRNA | ||
| Mg-159 | 1.23 | –3.19 |
| Mg-160 | 3.58 | –1.24 |
| Mg-161 | 1.75 | –2.40 |
| Mg-163 | 1.70 | –3.14 |
| Mg-164 | 2.60 | +1.64 |
| Mg-165 | 16.10 | +0.22 |
| Mg-166 | 6.28 | –0.16 |
| Mg-167 | 1.13 | –3.11 |
| Mg-168 | 2.63 | +0.22 |
| Mg-172 | 3.26 | –2.28 |
| Mg-173 | 1.53 | –3.26 |
| Mg-174 | 2.94 | –2.49 |
| Mg2+ Riboswitch | ||
| Mg-201 | 1.96 | –1.31 |
| Mg-202 | 2.09 | –3.00 |
| Mg-203 | 5.08 | –0.90 |
| Mg-204 | 12.21 | –1.07 |
| Mg-205 | 6.16 | –0.99 |
| Mg-206 | 14.32 | 0.00 |
a
Mg2+ residue labels are shown as they are listed in each PDB file.