Fig. 4: Binding mode analysis of AdaV/dAMP system by MD simulations.
From: Discovery and substrate specificity engineering of nucleotide halogenases
a Representative structure of binding mode 1. The iron atom (brown), oxo group (red), and chloride (green) are shown as spheres. Dotted cycles highlight the phosphate binding site. b Representative structure of binding mode 2. c Statistical analysis of distances between reacting atoms, i.e., dC2′-Cl and dO-H (in Å). Data are presented as mean ± s.d. Square symbols represent the mean distances and the error bars indicate the standard deviation of the mean. d Statistical analysis of substrate binding modes and productive conformations. P1 represents the percentage of binding modes in total frames. P2 denotes the percentage of productive conformations for each mode in total frames. Source data are provided in Source Data file.
