From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase

Figure 11

Top: the AMP-binding pocket viewed from the inside of the molecule. A solvent-accessible surface was created without the bound AMP, and then the final refined AMP model was superimposed. The noncovalently bound AMP is trapped within a closed compartment, which conforms well to the shape of the AMP molecule. Bottom: surface representation around the hole in the active site pocket. The surface of motif VI is colored cyan. The bound AMP is depicted as a sphere model. The phosphate (phosphorus, orange; oxygen, red) group is visible through a small “exit.”