An Introduction to Biomolecular Graphics
Figure 2
The active site of Mycobacterium tuberculosis dUTPase.
The orientation of the active site of this dUTPase (PDB 1SIX; [35]) was chosen to feature the geometry of the reaction it catalyzes, specifically the in-line nucleophilic attack of water 212 on the alpha-phosphate of dUTP. The orientation was fine-tuned to eliminate overlap of side chains and to make all hydrogen bonds (dashed lines) visible. Only side chains directly involved in catalysis are depicted. Carbons are colored according to five conserved motifs of the dUTPase family. Non-conserved residues are given a less-distracting gray color and are veiled in fog. Label colors match the side chains being labeled.