# Crystal Structure of Human Lysozyme Complexed with \(N\)-Acetyl-\(\alpha\)-D-glucosamine
## 3 Results and Discussion  
### Overall Structure  
All hLZM crystals belonged to the orthorhombic space group P212121, occupying one molecule in an asymmetric unit. The crystal structures of a native and two hAG-bound hLZM crystals were determined at 1.30 and 1.55/1.60 A resolution, respectively. The electron density was very clear for most of the residues between Lys19 and Val148 of all hLZM proteins, but not for Arg59-Ala60 of the native hLYZ. Validation of the geometry showed that >96% of the hLZM residues were within the most favored region of the Ramachandran plot and without outlier residues (Table 1). As hLZM contains eight cysteine residues that form disulfide bonds (Cys24-Cys146, Cys48-Cys134, Cys83-Cys99, and Cys95-Cys113), the lack of a significant negative Fo-Fc electron-density map indicated that all the hLZM structures determined in the current study were in an oxidized state. The  
\begin{table}
\begin{tabular}{c c c c} \hline \hline
**Data Collection** & **hLZM** & **hLZM-NAG1** & **hLZM-NAG2** \\ \hline Wavelength (Å) & 0.979 & 0.979 & 0.979 \\ Space group & P2121211 & P212121 & P2121211 \\ Unit cell dimension (Å) & & & \\ a & 33.035 & 32.796 & 32.980 \\ b & 56.062 & 55.758 & 56.049 \\ c & 61.063 & 60.859 & 60.939 \\ Resolution range (Å) a & 50.0–1.30(1.32–1.30) & 50.0–1.55 (1.58–1.55) & 50.0–1.60 (1.63–1.60) \\ Unique reflections & 28,633 (1358) & 16,579 (797) & 15,319 (688) \\ Completeness (\%) & 99.5 (94.8) & 99.6 (98.2) & 99.3 (90.3) \\ Redundancy & 6.4 (4.4) & 9.5 (5.0) & 6.0 (4.6) \\ Mean \(1/\sigma(l)\) & 40.42 (4.53) & 23.20 (3.37) & 27.59 (3.23) \\ R\({}_{\text{merge}}\) & 0.095 (0.428) & 0.293 (1.637) & 0.108 (0.524) \\ CC1/2 & 0.989 (0.863) & 0.981 (0.502) & 0.993 (0.832) \\ CC\({}^{\star}\) & 0.997 (0.963) & 0.995 (0.818) & 0.998 (0.953) \\ \hline
**Refinement** & & & \\ \hline Resolution range (Å) & 50.0–1.30 & 50.0–1.55 & 50.0–1.60 \\  & (1.33–1.30) & (1.60–1.55) & (1.65–1.60) \\ R\({}_{\text{work}}\) & 0.1513 (0.2055) & 0.1686 (0.2236) & 0.1683 (0.2034) \\ R\({}_{\text{free}}\) & 0.1710 (0.2056) & 0.1910 (0.2664) & 0.1844 (0.2572) \\ RMS deviations & & & \\ Bonds (Å) & 0.022 & 0.009 & 0.006 \\ Angles (degree) & 1.639 & 1.146 & 0.902 \\ Average \(B\) factor (Å\({}^{2}\)) & & & \\ Protein & 12.30 & 15.19 & 17.95 \\ Ligand & & 26.48 & 32.57 \\ Water & 24.01 & 25.01 & 27.55 \\ Ramachandran plot & & & \\ Most favored (\%) & 97.66 & 96.09 & 96.88 \\ Allowed (\%) & 2.34 & 3.91 & 3.12 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Data collection and refinement statistics.  
hLZM was composed of seven \(\alpha\)-helices and two \(\beta\)-strands, forming one \(\alpha\)-domain and one \(\beta\)-domain (Figure 1a). The approximate dimensions of hLZM were 30 \(\times\) 30 \(\times\) 45 A (Figure 1a). The active site of hLZM can accommodate six consecutive sugars at subsites A-F [2]. The catalytic residues Glu53 and Asp71 cleave the bond between subsites D and E (Figure 1b). The electrostatics of the active site of hLZM revealed a strong negatively charged surface (Figure 1b). The acetate ion of native hLZM was observed at subsite C and the \(\alpha\)-D-NAG molecule of the hLZM-NAG complex was observed in the middle of subsites C and D (see below).