ArticleNature protocols2018
Characterizing metal-binding sites in proteins with X-ray crystallography.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- PrOMet: Accurate and Robust Metal-Binding Site and Type Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy.Journal of chemical information and modeling · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- An autism spectrum disorder mutation in Topoisomerase 3β causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain.Nucleic acids research · 2025Article
- An autism spectrum disorder mutation in Topoisomerase 3β causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain.bioRxiv : the preprint server for biology · 2025Article
- Structure of theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Potential of Nanopore Technologies in Peptide and Protein Sensing for Biomarker Detection.Biosensors · 2025Review
- MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.Nature communications · 2025Article
- Lysosomal zinc nanomodulation blocks macrophage pyroptosis for counteracting atherosclerosis progression.Science advances · 2025Article
- Article
- Nickel binding to c-Src SH3 domain facilitates crystallization.bioRxiv : the preprint server for biology · 2025Article
- Status and perspective of protein crystallography at the first multi-bend achromat based synchrotron MAX IV.Journal of synchrotron radiation · 2025Article
- PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules.Nature communications · 2025Article
- The Coordination Chemistry of Two Peptidic Models of NFeoB and Core CFeoB Regions of FeoB Protein: Complexes of Fe(II), Mn(II), and Zn(II).Inorganic chemistry · 2025Article
- Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery.Expert opinion on drug discovery · 2025Review
- Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.Biochemistry · 2025Article
- Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization.Protein and peptide letters · 2025Article
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- Single-Molecule Electrical Profiling of Peptides and Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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