Fig. 3: Binding mode analysis of CtNTH/dGMP system by MD simulations and mutagenesis.
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. Arg99 is too far away to be included in the active site-focused figure. The figure including Arg99 can be found in SI (Supplementary Fig. 23c). 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. Suc stands for succinate. e Hydrogen bond occurrence between the substrate dGMP and the active site residues in mode 1. f Alanine mutation experiments of CtNTH. n = 3 biologically independent experiments. Data are presented as mean ± s.d. Source data are provided in Source Data file.
