Figure 5.

The acceptor binding site in B3GNT2.A, Difference density map (F_o-F_c, yellow mesh) for the acceptor lacto-N-neo-tetraose (LNnT, green) in the B3GNT2 acceptor binding cleft (pale gray surface), calculated at 1.85 Å and contoured at 3.0 σ. The map was calculated after omitting LNnT from the refined coordinates of B3GNT2:UDP:Mg²⁺:LNnT and subjecting the model to simulated annealing. The Gal and GlcNAc units of LNnT (Galβ(1–4)-GlcNAcβ(1–3)-Galβ(1–4)-Glc), the UDP (magenta), and Mg²⁺ (green sphere) are shown. B, The B3GNT2 active site (pale gray, cartoon) with UDP, LNnT, and Mg²⁺ depicted and colored as in Panel A. Residue side chains (sticks) that are involved in acceptor interactions and the loop insertions in the core GT-A fold (HV1 (cyan), HV2 (green), and HV3 (yellow) are shown. The xED motif, the location of the catalytic base in inverting GT-A fold GTs, is colored pink and Loop_β5-β6 (DxD motif) is colored slate blue. The side chain of the C-His involved in metal coordination is colored orange and the “Glycine-rich” loop is colored red. C, Ligplot (79) representation of the B3GNT2 active site showing the packing interactions (red, feathered lines) and hydrogen bonds (black, dashed lines) of the acceptor, LNnT (purple, ball and stick). The Gal and GlcNAc units of LNnT are highlighted in green.