1. Introduction

MetalMine is a database for metal ion binding proteins. As is indicated with the recent emergence of terms such as Metallome and Metallomics, the importance of metal ions in life system is attracting increasing attention. However, to our knowledge, there has been no complete list of metal binding proteins publicly available. Our objective is to prepare an organized list of functional metal binding sites. Efforts toward similar direction had been made at websites MDB [1] and Promise[2]. There are some excellent books such as a series edited by Messerschmidt et al.[3].

An automatic extraction of metal binding sites from PDB database results in many metal binding sites without biological function. These are typically result of the experimental conditions, such as salt added to enhance the crystallization. Although sometimes it is hard to make the distinction, we tried to exclude the artificial coordinations by manual curation.

2. Description

Metal binding sites are organized in a hierarchical manner. From the left side menu, you can browse by choosing kind of metal ions, metal binding sites(kind of proteins), and then each instance of metal coordination site in PDB structure. The metal binding site is displayed in a Jmol [4] window.

Metal binding sites are organized according to structural fold defined by SCOP database [5]. When only one metal site is found in a fold, and the metal binding site is identified with the name of the protein. Sometimes a SCOP fold contains more than one metal binding sites, terms are added to the name of the protein to distinguish them. For instance, a protein Peptidylglycine monooxygenase includes the CuH site and the CuM site.

The database can be searched by pdb id from the top page. Also, given an amino acid sequence, capability to perform a BLAST search to look for matches with metal binding residues in MetalMine, is available. There are some step by step guides in the Tutorial section.

3. References

[1] MDB: Metalloprotein Database and Browser

[2] PROMISE: The Prosthetic groups and Metal Ions in Protein Active Sites Database

[3] Handbook of Metalloproteins vol.1~3, editors:A.Messerschmidt, R.Huber, T.Poulos, K.Wieghardt, John Wiley and Sons

[4] Jmol: an open-soure Java viewer for chemical structures in 3D

[5] SCOP: Structural Classification of Proteins