The intricate interplay between metallocofactors and protein environments dictates the structure and function of metalloproteins. However, the complexity of their chemical interactions, influenced by multiple factors, poses significant challenges for both prediction and creation. To address this challenge, we have developed Metal-Installer, an in silico tool that facilitates metalloprotein design by guiding the incorporation of divalent transition metal-binding sites with atomic precision. By integrating geometric parameters derived from natural metalloproteins, Metal-Installer enables the creation of tailor-made metal coordination environments. Using this tool, we successfully designed and characterized thirteen artificial mononuclear and dinuclear metalloproteins, all of which aligned with our predictions and met minimal requirements for metal-dependent catalysis. This work significantly expands the accessible chemical space of metalloproteins beyond natural evolution, providing a versatile platform for synthesizing metalloenzyme mimics, biocatalysts, and protein-based materials.