The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB.
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The synthesis of the ligands N,N-bis [(2-pyridyl)methyl]-1-(2-pyridyl)ethanamine (1, R-MeTPA), N,N-bis[(6-phenyl-2-pyridyl)methyl]-1-(2-pyridyl)ethanamine (2, R-MePh 2 TPA), N,N-bis[(2-quinolyl)methyl]-1-(2-pyridyl)ethanamine, (3, R-MeBQPA), and N,N-bis[(2-pyridyl)]methyl(phenyl)(2-pyridyl)methanamine (4, R-PhTPA) is described. The ligands form chiral, pseudo C 3 -symmetric complexes with Zn II and Cu II salts that possess an available electrophilic coordination site. X-ray crystallographic structures of the complexes [Zn(R-MeTPA)Cl](ClO 4 ), [Zn(RMeBQPA)Cl](ClO 4 ), and [Zn(R-PhTPA)Cl]( ClO 4 ) show that the spatial arrangement of the three pyridyl groups resembles a propeller whose directional sense is controlled by a substituent on one methylene arm. Chiroptical measurements provide supporting information that the complexes maintain similar structures in solution. Monte Carlo/stochastic dynamics (MC/SD) simulations of the [Zn(L)Cl] + complexes indicate that only two conformers are populated at normal temperatures, suggest the presence of a synchronicity in the movement of the heteroaromatic rings during conformer interconversions, and provide an estimate of the energy difference between the conformers.
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