Rubredoxin description

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Table 1. Hydrogen bonds in alpha-helix of Enterococcus faecalis's Predicted transcriptional regulator* and beta-layer of protein Rubredoxin
# Atoms Bond's length, Å Angle N-O-C, °
Alpha-helix
1 N(048LEU)-O(044LEU) 2,76 160,6
2 N(049ALA)-O(045THR) 3,04 149,3
3 N(052GLU)-O(048LEU) 2,86 153,6
Beta-layer
1 N(050GLU)-O(005THR) 2,99 153,2
2 N(005THR)-O(050GLU) 2,76 156,5
3 N(013TYR)-O(004TYR) 2.71 167,3

*This protein is required because the initial one doesn't alpha-helixes of sufficient lengths (everything is obscure in it). The PDB entry is 3TYS.

Different sources provide various information about the hydrogen bond length and N-O-C angle. The most recurrent parameters found in literature are 2.9 Å and 135°. The acquired data perform deviation from the latter. The medium hydrogen bond's length is 2,89 Å for alpha-helix and 2,82 Å for beta-layer, both values differ from the standard by 0,01 Å and 0,08 Å respectively. The medium angle in alpha-helix is 154,5° and in beta-layer it is 159,0°. So the difference is 19,5° and 24°. Should one be amazed?! –It can not be said for sure because the statistical tests are not applicable in such cases.

Sources:

  1. Lehninger Principles of Biochemistry (Russian edition)

  2. www.sciencedirect.com

  3. proteinstructures.com