Figure 6.

Catalytic site interactions of CDP and F₂dCDP taken from Xu et al., PNAS 2006. (A) Stereo view of CDP (orange). Interacting atoms: oxygen, red; nitrogen, blue; phosphate, magenta; sulfur green; substrate carbons, cyan; protein non-Cα, yellow; Cα, as secondary structure, orange. (B) Stereo view of F₂dCDP. Interacting atoms are colored as in (A) above except sulfur orange; Cα carbons, as secondary structure, yellow; fluorines, grey. (C) Ligand plot of CDP ribose interactions. Colors are as in Figure 6(A), except that carbons are yellow and fluorine, black. (D) Ligand plot of F₂dCDP interactions. The van der Waals contact to L427 is omitted for clarity. (E) Stereo view of loop 2 superposition of AMPPNP-CDP (orange) and AMPPNP-F₂dCDP (yellow). Substrate/inhibitor is seen on the left and the effector is on the right. Reproduced with permission from PNAS. Copyright (2006) National Academy of Sciences, USA [84].