The ligand-binding site library.

A. Binding site examples. The Mg²⁺ ion is shown as a sphere; small molecules and protein residues are shown as sticks; carbon atoms are colored in green (small molecule) or grey (protein residues); oxygen atoms are colored in red; nitrogen atoms are colored in blue; polar interactions are shown as yellow dashed lines. B. Joint distribution of binding site sizes (numbers of binding site protein residues) and numbers of ligand heavy atoms. Binding site sizes are linearly correlated with the numbers of ligand heavy atoms. C, D. Amino acid (AA) frequencies (red, right y-axis) in ligand-binding sites and enrichment ratios (blue, left Y-axis) in ligand-binding sites compared to all residues in a protein. C. Distributions of all ligand binding sites. D. Distributions of single heavy atom ligand binding sites.