Cat_Wiz: A stereochemistry-guided toolkit for locating, diagnosing and annotating Mg2+ ions in RNA structures.

Abstract

Misassigned Mg2+ 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 Mg2+ 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 Mg2+ 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 [A] resolution Escherichia coli ribosome and from surveys of the Cambridge Structural Database. These principles provide a robust experimental foundation for characterizing Mg2+ 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 Mg2+-dependent backbone folds. Cat_Wiz is also applicable to Mg2+ binding sites in proteins and all related biomolecular systems since it is based on universal stereochemical principles.