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Denticity
About: Denticity is a research topic. Over the lifetime, 17851 publications have been published within this topic receiving 309492 citations.
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TL;DR: The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families, implying the preferred mechanistic pathway for activating the water will be determined by the identity of the other three ligands and their spacing.
Abstract: The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing.
412 citations
TL;DR: Lanthanide atom sizes (the lanthanide contraction) directly control the type of structure formed by the coordination of a single multidentate ligand, 3,5-pyrazoledicarboxylic acid (H(3)pdc).
Abstract: Lanthanide atom sizes (the lanthanide contraction) directly control the type of structure formed by the coordination of a single multidentate ligand, 3,5-pyrazoledicarboxylic acid (H3pdc). Single-layer, double-layer ([Eu2(Hpdc)3(H2O)6], see picture), and three-dimensional networks were found. Control of the reaction pH plays a key role in the structure formation in this system.
411 citations
TL;DR: In this paper, the design and preparation of stable cyanide-bearing six-coordinate complexes of formula [MIII(L)(CN)x](x+l−−m)− (M = trivalent transition metal ion and L = polydentate blocking ligand) are summarized and the appropriate choice of the end-cap ligand L whose denticity determines the number of coordinated cyanide groups in the mononuclear precursors.
405 citations
TL;DR: A review of the literature on the metal ion complexes of carbohydrate type ligands with the emphasis on the past 20 years, discussing the equilibria and structure in aqueous solution together with the structures determined for the solid state complexes are collected for comparison as discussed by the authors.
390 citations
TL;DR: The protein structure restricts access to the Fe site such that the formation of an organo-Fe intermediate seems improbable, and structural restrictions pertinent to other proposed reaction intermediates, such as planar pentadienyl and nonplanar allyl radicals, are discussed.
Abstract: Lipoxygenases, which are widely distributed among plant and animal species, are Fe-containing dioxygenases that act on lipids containing (Z,Z)-pentadiene moieties in the synthesis of compounds with a variety of functions. Utilizing an improved strategy of data collection, low temperature, and synchrotron radiation of short wavelength, the structure of ferrous soybean lipoxygenase L-1, a single chain protein of 839 amino acid residues, has been determined by X-ray crystallography to a resolution of 1.4 A. The R-factor for the refined model is 19.7%. General features of the protein structure were found to be consistent with the results of prior crystallographic studies at lower (2.6 A) resolution. In contrast to the prior studies, the binding of a water molecule to the active site Fe was established. The octahedral coordination sphere of the Fe also includes the side chains of His499, His504, His690, and Asn694 as well as the terminal carboxylate of Ile839, which binds as a monodentate ligand. Asn694 is inv...
388 citations