Table 6. Atoms close to the Glu166/OE1 in Class A β-lactamase after superimposition of the partial motifs.
1E25 | 2J7V | 2J9O | 1NZO | ||||||||
D | Residue | Atom | D | Residue | Atom | D | Residue | Atom | D | Residue | Atom |
0 | Glu166 | OE1 | 1.6 | Pro159 | C | 1.6 | Pro159 | C | 1.4 | LEU153 | CD2 |
1.3 | Glu166 | CD | 1.6 | Pro159 | CA | 1.6 | Pro159 | CA | 2.7 | LEU153 | CG |
2.2 | Glu166 | OE2 | 1.8 | Pro159 | O | 1.9 | Glu158 | OE1 | 2.8 | HOH475 | O |
2.4 | Glu166 | CG | 2.4 | Leu158 | CD1 | 1.9 | Pro159 | O | |||
2.7 | Glu166 | CB | 2.7 | Asp160 | N | 2.6 | Asp160 | N | |||
3 | Glu166 | CA | 2.7 | Pro159 | N | 2.7 | Glu158 | CA | |||
3.1 | HOH2076 | O | 2.7 | Leu158 | CA | 2.7 | Pro159 | N | |||
2.8 | Pro159 | CB | 2.8 | Glu158 | CB | ||||||
2.9 | Leu158 | CB | 2.8 | Glu158 | CD | ||||||
3.1 | Leu158 | CG | 2.9 | Pro159 | CB | ||||||
3.2 | Leu158 | C | 3.1 | Glu158 | C | ||||||
3.4 | HOH2146 | O | 3.3 | HOH2234 | O |
PDBid:1E25 is the Class A Blase, PDBid:2J7V is the wildtype PBP-A, PDBid:2J9O is the L158E PBP-A mutant and PDBid:1NZO is the PBP-5 protein. It can be seen that in the Class A Blase (PDBid:1E25) and PBP-5 there are no atoms within a radius of about 3 Å of Glu166/OE1. In the mutant L158E PBP, both Pro159 and Asp160 are spatially close to Glu158, and can be seen to be obstructing access to substrate (Fig. 4). Distances are in Å, and have a cut-off till the first water molecule is encountered.