Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus

The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, L-amino acid oxidase, kallikrein, phospholipase A(2) and myotoxic activities. The catalytically inactive PLA(2) homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972 Da, consists of 121 amino-acid residues crosslinked by seven disulfide bridges and shares high sequence homology with Lys49-PLA(2)s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49 -> Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA(2), from Zhaoermia mangshanensis venom at 2.05 A resolution, which represents a novel member of phospholipase A(2) family. In this structure, unlike the Lys49 PLA(2)s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA(2)s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the N zeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop. (c) 2008 Elsevier Ltd. All rights reserved.

Hydrothermal synthesis and crystal structure of a copper(ii) coordination polymer with bridging dicarboxylate and diamine ligands

This work reports on the synthesis of a copper(II) coordination compound with 4,4-oxibis(benzoate) (obb) and trans-1,2- bis(4-pyridyl)ethene (bpe) ligands. The complex was characterized by single-crystal X-ray diffraction, which showed a 3D polymeric structure. Each copper center is surrounded by four oxygen atoms at the basal plane and one nitrogen atom and one copper atom at the axial positions, revealing a distorted octahedral geometry. Four carboxylic groups bridge two copper atoms, forming a cage-like structure, with the distance between the metallic centers being 2.656(1)Å. 2008 © The Japan Society for Analytical Chemistry.

Coordination of construction behavior in the termite Procornitermes araujoi: structure is a stronger stimulus than volatile marking

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Antimycobacterial and antitumor activities of Palladium(II) complexes containing isonicotinamide (isn): X-ray structure of trans-[Pd(N-3)(2)(isn)(2)]

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Synthesis, X-ray structure and antimycobacterial activity of silver complexes with alpha-hydroxycarboxylic acids

In this paper, synthesis, characterization and antimycobacterial properties of a new water-soluble complex identified as silver-mandelate are described. Elemental and thermal analyses are consistent with the formula [Ag(C6H5C(OH)COO)](n). The polymeric structure was determined by single X-ray diffraction and the two-dimensional structure is based on the bis(carboxylate-O,O') dimer [Ag-O, 2.237(3), 2.222(3) angstrom]. The structure is extended along both the b and c axes through two oxygen atoms of a bidentate alpha-hydroxyl-carboxylate residue [Ag-OH(hydroxyl), 2.477(3) angstrom; Ag-O(carboxylate), 2.502(3) angstrom; O-Ag-O, 63.94(9)degrees]. A strong d(10)-d(10) interaction was observed between two silver atoms. The Ag...Ag distance is 2.8307(15) angstrom. The NMR C-13 spectrum in D2O shows that coordination of the ligand to Ag(l) occurs through the carboxylate group in solution. Potentiometric titration shows that only species with a molar metaHigand ratio of 2:2 are formed in aqueous solution. The mandelate complex and the silver-glycolate, silver-malate and silver-hydrogen-tartarate complexes were tested against three types of mycobacteria, Mycobacterium avium, Mycobacterium tuberculosis and Mycobacterium kansasii, and their minimal inhibitory concentration (MIC) values were determined. The results show that the four complexes are potential candidates for antiseptic or disinfectant drugs for discharged secretions of patients affected with tuberculosis. (c) 2006 Published by Elsevier B.V.

A tellurium-based cathepsin B inhibitor: Molecular structure, modelling, molecular docking and biological evaluation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The structure and optical dispersion of the refractive index of tellurite glass

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the quick cryo-soaking technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)(8) barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu(32), Asp(34), Asp(91), and solvent molecules. In the proposed acid base catalytic mechanism, His(12) and His(47) play key roles and are supported by a network of hydrogen bonds between Asp(34), Asp(52), Trp(230), Asp(233), and Asn(252).

1,3-dipolar cycloaddition of CS2 to the coordinated azide in the cyclopalladated [Pd(bzan)(mu-N-3)](2). Crystal and molecular structure of di(mu-N,S-1,2,3,4-thiatriazole-5-thiolate)bis[(benzylideneaniline-C-2,N)palladium(II)]

The compound [Pd(bzan)(mu -N-3)](2) 1, bzan = benzylideneaniline, was prepared from [Pd(bzan) (mu -OOCCH3)](2) by an anion exchange reaction. The 1,3-dipolar cycloaddition of carbon disulfide to the bridged coordinated azide in the cyclometallated compound I was investigated. The species resulting from this reaction, di(mu -N,S-1,2,3,4-thiatriazol-5-thiolate)bis[(benzylideneaniline)palladium(II)] 2, was characterized by IR spectroscopy and X-ray diffraction. The compound 2 is a dimer containing two [Pd(benzylideneaniline)] moieties connected by two vicinal bridging N,S-1,2,3,4-thiatriazole-5-thiolate anions in a square-planar coordination geometry for the palladium atoms.

Crystal structure and infrared analysis of a new trinuclear platinum(II) complex with L-cysteine

A new trinuclear platinum(II) complex with cysteine of composition [Pt(C3H6NO2S)Cl](3)center dot(C2H6SO)(3) was obtained and structurally characterized by X-ray diffraction and infrared analysis. The compound crystallizes in the trigonal system, space group R3, and is described in a hexagonal cell with a=17.739(1), c=9.531(1) and Z=3. Cysteine is coordinated to Pt(II) through the nitrogen and sulphur atoms. Each cysteine sulphur bridges between two metal atoms. A square planar coordination sphere of platinum is completed by a chlorine atom. The complex is soluble in dimethyl sulfoxide.

Cycloaddition reaction of the azido-bridged cyclometallated complex [Pd(dmba)N-3](2) with CS2. Crystal and molecular structure of DI(mu, N,S-1,2,3,4-thiatriazole-5-thiolate) bis[(N,N-dimethylbenzyl-amine-C-2,N)palladium(II)]

The 1,3-dipolar cycloaddition of carbon disulfide to the coordinated azide in the cyclometallated compound [Pd(dmba)(N-3)](2) (1), dmba = N,N-dimethylbenzylamine, was investigated. The compound obtained di(mu, N,S-1,2,3,4-thiatriazole-5-thiolate)-bis[(N,N-dimethylbenzylamine-C-2,N)palladium(II)] (2), was characterized by IR spectroscopy and X-ray diffraction. Complex (2) is dimeric with the two [Pd(N,N-dimethylbenzylamine)] moieties being connected by the two vicinal bridging N,S-1,2,3,4-thiatriazole-5-thiolate anions in a square-planar coordination for the palladium atoms.

Mono- and dinuclear palladium(II) compounds containing nitrogen ligands. Crystal and molecular structure of [Pd(N,C-dmba)(NCO)(2,3-lut)] and [Pd(H2CCOMe)Cl(2,2 '-bipy)]

The cyanate-bridged cyclopalladated compound [Pd(N,C-dmba)(mu-NCO)](2) (1) (dmba = PhCH2NMe2) reacts in CH2Cl2 with 2,3-lutidine (2,3- lut), 3,4-lutidine (3,4-lut), 2,2'-bipyridine (2,2'-bipy) and 4,4'-bipyridine (4,4'-bipy), to give [Pd(N, C-dmba)(NCO)(2,3-lut)] (2), [Pd(N,C-dmba)(NCO)(3,4-lut)] (3), [{Pd(N,C-dmba)(NCO)}(2)(mu-2,2'-bipy)] .CH2Cl2 (4) and [{Pd(N,C-dmba)(NCO)}(2)(mu-4,4'-bipy)] . CH2Cl2 (5), respectively. The compounds were characterized by elemental analysis, i.r. and n. m. r. spectroscopy and also by t.g.a. The i.r. spectra of (2 - 5) display typical bands of monodentate N-bonded cyanate groups, whereas the n. m. r. data of (4) are consistent with the presence of a bridging 2,2'-bipyridine ligand. Complex (4) decomposes slowly in acetone. One of the products formed, [Pd(H2CCOMe) Cl(2,2'-bipy)] (6), was characterized by X-ray diffraction. As inferred from the t.g.a., the thermal stability decreases in the order: [{Pd(N,C-dmba)(NCO)}(2) (mu-4,4'-bipy)]. CH2Cl2 (5) > [Pd(N,C-dmba)(2,3-lut)( NCO)] (2) = [Pd(N, C-dmba)(3,4-lut)(NCO)] (3) > [{Pd(N,C-dmba)(NCO)}(2)(mu- 2,2'-bipy)] .CH2Cl2 (4). According to thermal analysis and X-ray diffraction patterns compounds (2 - 3) decompose into metallic palladium Pd(0), whereas (4 - 5) decompose with the formation of PdO. The X-ray crystal and molecular structure of [Pd(N, C-dmba)( NCO)(2,3-lut)] (2) was determined. The lutidine unit is perpendicular to the coordination plane.

Mixed pseudohalide complexes of copper(II). Crystal and molecular structure of [Cu(N-3)(NCS)(tmen)](n) and of [Cu(N-3)(NCO)(tmen)]2 (tmen = N,N,N ',N '-tetramethylethylenediamine)

The compounds [Cu(N-3)(NSC)(tmen)](n) (1), [Cu(N-3)(NCO)(tmen)](n) (2) and [Cu(N-3)(NCO)(tmen)](2) (3) (tmen = N,N,N',N'-tetramethylethylenediamine) were synthesized and studied by i.r. spectroscopy. Single crystals of compounds (1) and (3) were obtained and characterized by X-ray diffraction. The structure of compound (1) consists of neutral chains of copper(II) ions bridged by a single azido ligand showing the asymmetric end-to-end coordination fashion. Each copper ion is also surrounded by the other three nitrogen atoms: two from one N,N,N',N'-tetramethylethylenediamine and one from a terminal bonded thiocyanate group. Compound (2) decomposes slowly in acetone and the product formed [Cu(N-3)(NCO)(tmen)](2) (3) crystallizes in the monoclinic system (P2(1)). The structure of (3) consists of dimeric units in which the Cu atoms are penta-coordinated and connected by p(1,3) bridging azido and cyanate ligands. In both cases the five coordinated atoms give rise to a slightly distorted square-based pyramid coordination geometry at each copper ion. The thermal behavior of [Cu(N-3)(NSC)(tmen)](n) (1) and [Cu(N-3)(NCO)(tmen)](n) (2) were investigated and the final decomposition products were identified by X-ray powder diagrams.