Figure 3

Superimposition of vvUDG and E. coli UDG: Close-up view of the active site. The figure shows a close-up view of the active site of vvUDG and E. coli UDG. The two structures were superimposed with TOPP [22]. (A) Active site of vvUDG. The active site of vvUDG with the glycerol (GOL) molecule at the center is shown in this stereo figure. The difference electron density for glycerol (F_o-F_c omit map contoured at 3σ) is displayed (blue mesh). A second glycerol molecule away from the active site can also be seen. Active site residues are shown as stick models. (B) Active site of E. coli UDG (3EUG). Shown is a close-up view of the active site in E. coli UDG in the same orientation as the vvUDG in Fig. 3A. The bound glycerol (GOL) in the active site is shown in the center. Active site residues are shown as stick models. (C) Active site of vvUDG with modeled uracil. The active site of vvUDG was superimposed on the E. coli UDG active site containing uracil. The uracil molecule (URA) is modeled into the active site of vvUDG in the same position and orientation as seen in Fig. 3D for the E. coli structure (2EUG). The carbonyl oxygen atoms of uracil in this model superimpose with two hydroxyl groups in glycerol in the vvUDG structure. (D) Active site in E. coli UDG (2EUG). Shown is a close-up view of the active site in E. coli UDG with a bound uracil (URA) molecule in the same orientation as in Figs. 3A and 3B.