2007/07/26 by Mariana Babor, Sergey Gerzon, Barak Raveh +3
Biochemistry, Genetics and Molecular Biology · Materials Science · Nursing · #Enzyme Structure and Function #Protein Structure and Dynamics #Trace Elements in Health
paper · doi:10.1002/prot.21587
openalex publication_date 2007/07/26 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
Metal ions are crucial for protein function. They participate in enzyme catalysis, play regulatory roles, and help maintain protein structure. Current tools for predicting metal-protein interactions are based on proteins crystallized with their metal ions present (holo forms). However, a majority of resolved structures are free of metal ions (apo forms). Moreover, metal binding is a dynamic process, often involving conformational rearrangement of the binding pocket. Thus, effective predictions need to be based on the structure of the apo state. Here, we report an approach that identifies transition metal-binding sites in apo forms with a resulting selectivity >95%. Applying the approach to apo forms in the Protein Data Bank and structural genomics initiative identifies a large number of previously unknown, putative metal-binding sites, and their amino acid residues, in some cases providing a first clue to the function of the protein.