Protein-metal binding databases | Interaction data analysis
It has been estimated that 30–40% of proteins require one or more metal ions to be able to carry out their biological function in cells. This proportion depends on the specific organism or tissue under consideration, which affects also the relative usage of the various metals. Additionally, metal ions play a decisive role in stabilizing the structure of nucleic acids.
Collects information related to metal sites in biological macromolecules. MetalPDB starts from the structural information contained in the Protein Data Bank (PDB) with the aim of providing an access to an overview of metal-containing biological structures. Searches can be made by keywords, metal, sequence, or PDB List. The database includes panels that give access to a direct downloading, links towards tools dedicated to metal analysis, and various statistics. The repository is updated monthly in an automated manner.
A web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion-donor distance and percentage of the selected metal ions coordinated by each of the selected ligands.
Compiles the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 A radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.
Represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM), 'molecule' (MOL), and 'complex proteins' (PRX), with each entity being assigned a unique identifier. The complex proteins in COMe are subdivided into three categories: (i) metalloproteins, (ii) organic prosthetic group proteins and (iii) modified amino acid proteins.
A database of metals in the three-dimensional macromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed database serves as an open resource for the analysis and visualization of all metals and their interactions with macromolecular (protein and nucleic acid) structures. MIPS can be searched via a user-friendly interface, and the interactions between metals and protein molecules, and the geometric parameters, can be viewed in both textual and graphical format using the freely available graphics plug-in Jmol.
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