Table 2.
RMS coordinate fluctuations (Å) from molecular dynamics of sugars bound to barley chitinase*
| Conformation | Binding subsite | |||||
|---|---|---|---|---|---|---|
| A | B | C | D | E | F | |
| hexaNAG | 0.908 | 0.498 | 0.458 | 0.405 | 0.531 | 0.486 |
| tri-NAg-oxocarbenium | 0.501 | 0.447 | 0.384 | 0.411 | — | — |
| tri-NAG-oxazoline | 0.411 | 0.340 | 0.381 | 0.450 | — | — |
*
The hexaNAG substrate binding and two TriNAG intermediates were considered. RMS coordinate fluctuations were calculated as follows: The average structure for the MD interval from 30 to 100 ps was determined. The RMS coordinate difference between this average structure and snapshots taken every 5 ps from 30 to 100 ps were determined. The average of this RMS is reported separated by sugar residue.