Recent updates to CheckMyMetal have significantly enhanced its capability to efficiently handle large datasets, including those generated from cryo-EM structural analyses.

The crystal structures of CutA1 from T. thermophilus HB8 with and without bound Na⁺ and CutA1 from P. horikoshii OT3 in complex with Na⁺ have been determined in order to understand metal binding and metal-driven assembly features of the proteins.

YfeA, a substrate-binding protein that is important for the virulence of Yersinia pestis, has two polyspecific metal-binding sites that may play different roles during infection. A flexible lobe at the carboxy-terminus suggests that structural rearrangement is required for metal transfer to binding partners.

The metal-site validation tool CheckMyMetal is described, with examples to follow.

The Yersinia pestis substrate-binding protein YfeA contains two polyspecific metal-binding sites, and site 2 is capable of collaborating with other protein molecules for inter-protein metal coordination. The inter-protein metal coordination can occur by multiple coordination geometries and may be flexible enough to enable metal transfer to multiple metal-binding proteins.

The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature.

A detailed analysis of rhenium(I) organometallic covalent binding to a model protein is conducted at seven time points over 38 weeks. Changes in the protein structure induced at the Re binding sites over the time series as well as the relationship between the proximity of the solvent channels to the residues containing the highest-occupied Re are described.

Through the analysis of more than 115 000 metal-binding sites in metalloproteins, experimentalists are offered useful reference data that improve the understanding of metal-binding interactions and protein coordination. Carboxylate coordination, which is common for a variety of metals, is especially highlighted.

The stepwise addition of Cu²⁺ ions to a nonplanar cyclic Schiff base yields a one-end-open dinuclear copper chelate with N₂O₂ and O₂O₂ coordination sites. The O₂O₂-bonded Cu atom has a coordination number of five, showing square-bipyramidal geometry around the Cu atom. The N₂O₂-coordinated site provides sufficient electron density to the other Cu atom to be stabilized with a coordination number of four, showing square-planar geometry around the Cu atom.

The structural and zinc-binding properties of PA4063, one of the periplasmic proteins expressed by Pseudomonas aeruginosa under zinc-deficient conditions, are presented. PA4063 has a noncanonical ferredoxin-like fold. Two zinc-binding sites with micromolar affinity are exposed and are located on the same face of the structure. Two histidine-rich loops, which are disordered in the apoprotein, contribute to zinc coordination in one of the sites. These findings strongly suggest a role for PA4063 in zinc trafficking, possibly acting as a metal chaperone or as a regulator of a transport system.