Figure 3. PhnY active site in complex with substrate PnAA, product PnA and cofactor NAD⁺.

All atoms are shown in ball-and-stick representation with PhnY side chain carbon atoms colored yellow, and PnAA, PnA and NAD⁺ carbon atoms colored green. (A) See also Supplemental Figure S2. Stereo view showing the active site features of PhnY in the binary complex with the substrate PnAA. Superimposed is a difference Fourier electron density map (contoured at 2.5σ over background in blue) calculated as before. Stabilizing interactions of PnAA with PhnY are shown as black dashes. (B) See also Supplemental Figure S3. Stereo view of the PhnY active site in the ternary complex with substrate PnAA and cofactor NAD⁺. Superimposed is the difference electron density map contoured at 2.5σ over background in blue, calculated as before. Note that the nicotinamide and ribose rings for the cofactor have not been modeled. (C) See also Supplemental Figures S4, S5. Stereo view of the PhnY active site in the ternary complex with product PnA and cofactor NAD⁺. Superimposed is a difference Fourier electron density map (contoured at 2.5σ over background in blue,) calculated as before. Stabilizing interactions for NAD⁺ are described in Supplementary Figure S4. Note the presence of the nicotinamide ring and the ribose sugar.