FIGURE 2.
Stereoviews of β-galactosidases with allolactose, Bis-Tris, and l-ribose ligands. Oxygen atoms are red, nitrogen atoms are blue, and water molecules are represented by red spheres. Carbon atoms from residues involved in Glc binding are green and the electron density (2Fo − Fc) is pale yellow and contoured at 1.5σ, those from Glu-461 and Trp-568 are white and the electron density is left out, and the carbon atoms of allolactose, Bis-Tris, and l-ribose are magenta. The dashed lines show the interactions between the enzyme and the compounds in the Glc site: black, H-bonds of 3.2 Å length or less; gray, H-bonds between 3.2 and 3.4 Å; red, C-H···π bonds between hydrogens on sugars and the π electrons of Trp-999 (note that there are probably more of these, only bonds with short distances are shown); orange, hydrophobic interactions; light blue, bonds with Glu-461. A, shown is G794A-β-galactosidase active site structure with a trapped allolactose. The electron density of the allolactose (2Fo − Fc) is contoured at 1σ. B, shown is the G794A-β-galactosidase active site structure with a covalently bound 2-deoxy-galactose (yellow carbons with the electron density left out for clarity) and Bis-Tris in the Glc binding site. The electron density of Bis-Tris (2Fo − Fc) is contoured at 1σ. C, N460S-β-galactosidase with l-ribose in the position normally occupied by Gal in the deep mode and a second l-ribose in the Glc binding site is shown. The l-ribose in the Gal position is shown as magenta lines and without electron density so as not to obscure the rest of the structure. The electron density of the l-ribose in the acceptor site is contoured at 0.8σ. To the right of each panel (A, B, and C) are two insets showing simulated annealing omit maps (Fo − Fc) contoured at 3σ. The orientation of the omit densities in the top inset is identical to that in the main panel. The lower inset is re-oriented to more clearly show the ligand fit to the electron density.