Fig. 3.

LpxB nucleotide-binding pocket. The uracil of UDP binds in a hydrophobic pocket formed by L197, P198, P231, and V233. Putative hydrogen-bond distances in angstroms are as follows: G199 N to uracil O4 (2.7), G199 O to water to uracil O4 (2.8, 3.2), V233 N to water to uracil O4 (3.0, 3.2), P231 O to uracil N3 (2.5), G261 N to water to uracil O2 (2.9, 2.9), E281 Oε2 to ribose O2' (2.5), E281 Oε2 to ribose O3' (2.4), S200 Oγ to α-phosphate O1 (3.2), S200 Oγ to α-phosphate O2 (2.9), T277 Oγ to bridging pyrophosphate O (2.9), and T277 Oγ to β-phosphate O2 (2.9). R201, which is critical for activity¹⁰, is interacting with the α-phosphate O2 and β-phosphate O1 at 3.8, via its η-nitrogens and appears to be positioned to stabilize the UDP leaving-group. a Image generated in LigPlot+⁶⁹. b Image generated in Coot⁶², showing the electron density maps for UDP and the surrounding residues. The 2mFo-DFc map (blue mesh) is shown at 0.4317 e Å⁻³ (0.99 r.m.s.d.), and the mFo-DFc map (cyan mesh for positive and yellow mesh for negative) is shown at 0.45 e Å⁻³ (3.01 r.m.s.d.). See Supplementary Figure 6 for stereo view. c Image generated in UCSF Chimera⁴⁹