Cat_Wiz: A stereochemistry-guided toolkit for locating, diagnosing and annotating Mg ²⁺ ions in RNA structures

Misassigned Mg ²⁺ ions are pervasive in RNA structural databases, obscuring mechanistic interpretation, undermining comparative analyses and compromising machine-learning training sets. Here, we present Cat_Wiz , a Coot -integrated, stereochemistry guided toolkit that facilitates the localization, diagnosis, correction and annotation of Mg ²⁺ binding sites. Cat_Wiz comprises three modules: MG_diagnosis which validates and regularizes existing assignments; MG_detect which identifies unmodelled ion binding sites; and MG_clamp which classifies recurrent Mg ²⁺ clamp motifs. Cat_Wiz also includes a complete binding site annotation system. The stereochemical principles implemented in Cat_Wiz were derived from an earlier analysis of the 1.55 Å resolution Escherichia coli ribosome and from surveys of the Cambridge Structural Database. These principles provide a robust experimental foundation for characterizing Mg ²⁺ binding sites. Applications to ribosomes, hammerhead ribozymes, group I introns, and quaternary RNA assemblies demonstrate that Cat_Wiz rapidly locates overlooked ions, corrects misassignments, and improves stereochemical fidelity in hours rather than days. Beyond refinement, Cat_Wiz generates curated data that can seed diverse machine-learning and AI models. This transparent, cost-effective framework establishes reproducible standards for RNA-ion assignments and will drive progress in the design of RNA 3D architectures through the identification of unique Mg ²⁺ -dependent backbone folds. Cat_Wiz is also applicable to Mg ²⁺ binding sites in proteins and all related biomolecular systems since it is based on universal stereochemical principles.