Protein visualisation
ruHigh Resolution Structure Of The Ni-R State Of [NiFe]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. Desulfovibrio vulgaris Desulfovibrio vulgaris is a species of Gram-negative sulfate-reducing bacteria in the Desulfovibrionaceae family. Desulfovibrio vulgaris is often used as a model organism for sulfur-reducing bacteria.
| # | O atom | H atom | Bond length, nm | Distance between N & O | N-O-C angle (°) |
|---|---|---|---|---|---|
| β-sheet | |||||
| 1 | [ILE]71:S | [VAL]10:S | 0.206 | 0.289 | 153.8 |
| 2 | [VAL]10:S | [VAL]73:S | 0.210 | 0.291 | 156.3 |
| 3 | [VAL]73:S | [LEU]12:S | 0.209 | 0.289 | 165.9 |
| 4 | [LEU]12:S | [GLU]75:S | 0.207 | 0.293 | 160.8 |
| 5 | [SER]8:S | [ILE]71:S | 0.202 | 0.286 | 159.1 |
| α-helix | |||||
| 1 | [GLN]119:L | [ASP]123:L | 0.206 | 0.291 | 162.1 |
| 2 | [ALA]118:L | [HIS]122:L | 0.220 | 0.304 | 160.2 |
| 3 | [GLY]117:L | [LEU]121:L | 0.241 | 0.323 | 156.3 |
Discussion
According to [2],average distance between N & O in α-helix is 2.99Å, in β-sheet - 2.91Å.
The data about β-sheet corresponds to the average of 2.9Å, dispersion is 0,00192, that answers previous data.
Variation in α-helix is much greater. The data corresponds to bond length equal to 0.304±0.017nm,
that is evident from [3]
According to [3] the N-O-C angle is most probable to be in ranges of 100-110 or 150-160deg. The data correspond it.
Thus, hydrogen bond parameters in the secondary structure elements are typical for proteins.
References:
[1]https://www.rcsb.org/structure/4u9i
[2] Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding
in globular proteins. Progr. Biophys. Mol. Biol. 44, 97-179
[3] D. F. Stickle et al. Hydrogen Bonding in Globular Proteins
[4] Ogata, H., Nishikawa, K., Lubitz, W. Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.
[5] https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris