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. 2013 Aug 1;8(8):e71077. doi: 10.1371/journal.pone.0071077

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.

a

PDB 2AM3 has a glycerol molecule modeled as an acceptor.

b

It is likely that the active species are not actually water molecules, but residues in disordered regions of the polypeptide.

c

b, c and f are octahedral binding partners to the coordinated metal atom M as described in Figure 2 .