Table 2. Active site residue identities and geometric values.
Stereospecificity | Inverting | Retaining | |||||
Example enzyme | GlcAT-I | GalT1 | GnT1 | LgtC | GTA | Extl2 | ManT |
PDB(1) | 1V84 | 1TVY | 2AM3 | 1GA8 | 2RJ7 | 1OMZ | 2WVL |
PDB(2) | 1KWS | 1TW5 | |||||
Nu – C1 dist. | 4.4 Å | 4.2 Å | 4.0 Åa | 2.2 Å | 2.5 Å | ||
<Nu-C1-O3 | 160° | 165° | 151°a | 90° | 74° | NA | NA |
Nu – O3 dist. | 5.8 Å | 5.6 Å | 5.4 Åa | 2.8 Å | 2.2 Å | ||
O3– nearest polar X | H2Ob | K279 | Y184 | H78 | K346 | H2Ob | Y268 |
O3- X dist. | 4.4 Å | 4.4 Å | 5.4 Å | 4.7 Å | 5.6 Å | 3.8 Å | 4.4 Å |
<X-O3-C1 | 91° | 80° | 87° | 171° | 149° | 131° | 59° |
C1 nearest polar Y | H308 | W314 | D211 | Q189 | E303 | R293 | D167 |
C1-Y dist | 3.6 Å | 4.5 Å | 5.2 Å | 3.5 Å | 4.8 Å | 3.7 Å | 3.5Å |
<Y-C1-O3 | 67° | 75° | 71° | 162° | 155° | 167° | 142° |
O5 nearest polar Z | R156 | W314 | D291 | Q189 | R352 | R293 | D168 |
O5-Z dist. | 5.9 Å | 3.4 Å | 3.9 Å | 4.2 Å | 5.8 Å | 3.2 Å | 3.8 Å |
<Z-O5-C1 | 113° | 123° | 96° | 82° | 83° | 97° | 68° |
c c | H2Ob | H2Ob | H2Ob | D103 | D211 | H2Ob | NA |
<bMc c | 89° | 82° | 87° | 105° | 116° | 101° | NA |
f c | D196 | H347 | H2Ob | D105 | D213 | H2Ob | N313 |
<bMf c | 114° | 104° | 95° | 92° | 90° | 88° | 82° |
With the exception of the GTA neutron diffraction studies [44] hydrogen atoms are not directly observed, so distances are given between centers of non-hydrogen atoms. Italic enzyme names indicate the model did not contain an acceptor molecule.
PDB 2AM3 has a glycerol molecule modeled as an acceptor.
It is likely that the active species are not actually water molecules, but residues in disordered regions of the polypeptide.
b, c and f are octahedral binding partners to the coordinated metal atom M as described in Figure 2 .