PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “ATOM complex”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources
PubMed1998

Cinoxacin complexes with divalent metal ions. Spectroscopic characterization. Crystal structure of a new dinuclear Cd(II) complex having two chelate-bridging carboxylate groups. Antibacterial studies.

Several cinoxacin (HCx) complexes with divalent metal ions have been prepared and characterized by spectroscopic techniques. The crystal structure of [Cd2(Cx)4(H2O)2].10H2O has been determined by X-ray diffraction. The complex is triclinic, space group P1 with unit-cell dimensions: a = 10.412(2), b = 11.119(2), c = 13.143(6)A, chi== 76.78(4) degrees, beta = 74.59(3) degrees, gamma = 77.12(3) degrees, V = 1406.0(8) A3. In this complex each cadmium atom is heptacoordinated: the metal environment is formed by two Oketo and two Ocarbox atoms from two different cinoxacinate monoanions, two carboxylate oxygen atoms from a third cinoxacinate ligand and by one water oxygen atom on the seventh position. Two of the cinoxacinate ions act as tridentate chelate and bridging ligands and the other one as a bidentate chelate ligand. In the bridging monoanions the carboxylate group is behaving as a chelate ligand. All the complexes were screened for their activity against several bacteria, showing activity similar to that of cinoxacin. Additionally, the number of bacteria killed after 3 h of incubation with cinoxacin, [Cu(Cx)2].2H2O and [Co(Cx)3]Na.10H2O complexes was determined against E. coli ATCC 25922; the copper compound presents paradoxical effect which has been described and related to the mechanism of action of quinolones.

4-Quinolones↗
PubMed1994

Atomic structure of the trypsin-A90720A complex: a unified approach to structure and function.

BACKGROUND: A90720A is a potent serine proteinase inhibitor produced by the terrestrial blue-green alga Microchaete loktakensis. Most of its structure has been defined by spectroscopic and degradative studies, but the configurations of several stereochemical centers are unknown, and its mode of inhibition of serine proteinases is not understood. We therefore examined the structure of the compound in a complex with trypsin. RESULTS: We have crystallized the bovine trypsin-A90720A complex and determined its three-dimensional structure at 1.90 A resolution using single crystal X-ray diffraction. The structure of the bound inhibitor is clearly shown in the electron density. The structure defines the absolute stereostructure of A90720A, establishes its bound conformation and illuminates its mode of inhibition. CONCLUSIONS: A90720A interacts with trypsin in a substrate-like manner through an extensive series of hydrogen bonds, hydrophobic interactions and steric complementarity. The compound uses a mixture of peptidal and nonpeptidal elements to imitate the canonical conformation of the exposed binding loop of 'small' proteinase inhibitors.

Animals↗
PubMed1999

Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head.

The crystal structure of a proteolytic subfragment from scallop striated muscle myosin, complexed with MgADP, has been solved at 2.5 A resolution and reveals an unusual conformation of the myosin head. The converter and the lever arm are in very different positions from those in either the pre-power stroke or near-rigor state structures; moreover, in contrast to these structures, the SH1 helix is seen to be unwound. Here we compare the overall organization of the myosin head in these three states and show how the conformation of three flexible "joints" produces rearrangements of the four major subdomains in the myosin head with different bound nucleotides. We believe that this novel structure represents one of the prehydrolysis ("ATP") states of the contractile cycle in which the myosin heads stay detached from actin.

Adenosine Diphosphate↗
PubMed2005

The C-H activation of methane by laser-ablated zirconium atoms: CH2=ZrH2, the simplest carbene hydride complex, agostic bonding, and (CH3)2ZrH2.

Reaction of laser-ablated Zr with CH(4) ((13)CH(4), CD(4), and CH(2)D(2)) in excess neon during condensation at 5 K forms CH(2)=ZrH(2), the simplest alkylidene hydride complex, which is identified by infrared absorptions at 1581.0, 1546.2, 757.0, and 634.5 cm(-)(1). Density functional theory electronic structure calculations using a large basis set with polarization functions predict a C(1) symmetry structure with agostic C-H- - -Zr bonding and distance of 2.300 A. Identification of the agostic CH(2)=ZrH(2) methylidene complex is confirmed by an excellent match of calculated and observed isotopic frequencies particularly for the four unique CHD=ZrHD isotopic modifications. The analogous reactions in excess argon give two persistent photoreversible matrix configurations for CH(2)=ZrH(2). Finally, methane activation by CH(2)=ZrH(2) gives the new (CH(3))(2)ZrH(2) molecule.

Journal Article↗
PubMed2000

Atomic structures of two nitroxide spin labels complexed with human thrombin: comparison with solution studies.

Crystal structures of thrombin complexed with two spin labels called para-V, 4-(2,2,5,5-tetramethylpyrrolidine-1-oxyl)-p-(fluorosulfonyl) benzamidine, and meta-V, 3-(2,2,5,5-tetramethyl-pyrrolidine1-oxyl)-m-(fluorosulfonyl) benzamidine, have been completed at 2.0 and 3.0 A resolution, respectively. Previous electron spin resonance studies with these labels gave rise to a low-resolution "topography map" of thrombin's extended active site. These labels monitor two distinct areas of the thrombin active site: (1) an apolar binding site which manifests itself in an biphasic activation/inhibition effect on thrombin activity and (2) a region sensitive to alpha-thrombin autoproteolytic cleavage(s) to gamma-thrombin (Arg75-Tyr76 and/or Arg77A-Asn78, and Lys149E-Gly150, chymotrypsin numbering). Para-V was found to bind along the substrate binding cleft, while meta-V was found to bind both at the substrate primary specificity pocket and at a site which interacts with the gamma-cleavage loop. These studies reaffirm that accurate information may be gained from solution studies and indicates the complementarity of solid-state studies.

Binding Sites↗
PubMed1994

Atomic model of plant light-harvesting complex by electron crystallography.

The structure of the light-harvesting chlorophyll a/b-protein complex, an integral membrane protein, has been determined at 3.4 A resolution by electron crystallography of two-dimensional crystals. Two of the three membrane-spanning alpha-helices are held together by ion pairs formed by charged residues that also serve as chlorophyll ligands. In the centre of the complex, chlorophyll a is in close contact with chlorophyll b for rapid energy transfer, and with two carotenoids that prevent the formation of toxic singlet oxygen.

Amino Acid Sequence↗
PubMed1999

Atomic structure of the GCSF-receptor complex showing a new cytokine-receptor recognition scheme.

Granulocyte colony-stimulating factor (GCSF) is the principal growth factor regulating the maturation, proliferation and differentiation of the precursor cells of neutrophilic granulocytes and is used to treat neutropenia. GCSF is a member of the long-chain subtype of the class 1 cytokine superfamily, which includes growth hormone, erythropoietin, interleukin 6 and oncostatin M. Here we have determined the crystal structure of GCSF complexed to the BN-BC domains, the principal ligand-binding region of the GCSF receptor (GCSFR). The two receptor domains form a complex in a 2:2 ratio with the ligand, with a non-crystallographic pseudo-twofold axis through primarily the interdomain region and secondarily the BC domain. This structural view of a gp130-type receptor-ligand complex presents a new molecular basis for cytokine-receptor recognition.

Amino Acid Sequence↗
PubMed1979

Atomic resolution analysis of a 2:1 complex of CpG and acridine orange.

Cytidylyl-3', 5'-guanosine and acridine orange crystallize in a highly-ordered triclinic lattice which diffracts X-rays to 0.85 angstrom resolution. The crystal structure has been solved and refined to a residual factor of 9.5%. The two dinucleoside phosphate molecules form an antiparallel double helix with the acridine orange intercalated between them. The two base pairs of the double helical fragment have a twist angle of 10 degrees and it is found to have a C3' endo-(3', 5')-C2' endo mixed sugar puckering along the nucleotide backbone as has been observed for other simple intercalator complexes. Twenty-five water molecules have been located in the lattice together with a sodium ion. The intercalator double helical fragments form sheets which are held together by van der Waals interactions in one direction and hydrogen bonding interactions in the other. The crystal lattice contains aqueous channels in which sixteen water molecules are hydrogen bonded to the nucleotide, none to the intercalator, five water molecules are coordinated about the sodium ion and four water molecules bind solely to other water molecules. The bases in the base pairs have a dihedral angle of 7 to 8 degrees between them.

Acridine Orange↗
PubMed2006

Bis(ethylenediaminium) bis[oxalohydroxamato(3-)]nickelate(II) dihydrate.

The title compound, (C2H10N2)2[Ni(C2HN2O4)2].2H2O, has an ionic structure containing a centrosymmetric complex 4- anion, charge-balancing ethylenediaminium dications and solvent water molecules. The oxalohydroxamate unit is triply deprotonated and forms five-membered chelate rings with the central Ni ion; the Ni ion lies on an inversion centre. The two hydroxamate O atoms in the complex anion are linked by short intramolecular hydrogen bonds.

Crystallography, X-Ray↗
PubMed2001

Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics.

Many three-dimensional structures of retaining beta-D-glycoside hydrolases have been determined, yet oligosaccharide complexes in which the ligand spans the catalytic centre are rare. Those that have been reported so far have revealed two modes of binding: those in which the substrate adopts a distorted skew-boat or envelope conformation in the -1 subsite, reflecting the distortion observed during the catalytic cycle, and those which bypass the true catalytic centre and thus lie in a non-productive manner across the -1 subsite. The three-dimensional structure of a retaining endocellulase, Bacillus agaradhaerens Cel5A, in complex with methyl 4,4(II),4(III),4(IV)-tetrathio-alpha-cellopentoside falls into this latter category. The 1.1 A structure reveals the binding of five pyranosides, all in the (4)C(1) chair conformation, occupying the -3, -2, +1 and +2 subsites whilst evading the catalytic machinery located in the true -1 subsite. Such binding is in marked contrast to the structure of another retaining endocellulase, the Fusarium oxysporum Cel7B, the identical ligand in which displayed a distorted skew-boat conformation at the active centre. These two binding modes may reflect different steps in the binding and catalytic process.

Bacillus↗
PubMed2003

Synthesis and comprehensive characterizations of new cis-RuL(2)X(2) (X = Cl, CN, and NCS) sensitizers for nanocrystalline TiO(2) solar cell using Bis-phosphonated bipyridine ligands (L).

The preparation and the properties of several ruthenium complexes of the general formula cis-RuL(2)X(2) with L = 2,2'-bipyridine-4,4'-bisphosphonic acid, L' = 2,2'-bipyridine-5,5'-bisphosphonic acid, and X = Cl, CN, or NCS are reported. The synthesis of these complexes relies on the preparation of the key intermediates cis-Ru(bipyridinebis(diethyl ester phosphonate))Cl(2). The ground-state second pK(a) values of the thiocyanato complexes were determined and are 6.0 and 6.1 for cis-RuL(2)(NCS)(2) and for cis-RuL'(2)(NCS)(2), respectively. For these species, (13)C NMR and IR demonstrate that the thiocyanato ligands are bound to Ru via the N atom. The new complexes exhibit a blue-shifted electronic absorption spectrum with respect to the analogous complexes containing carboxylic acid groups. Density functional theory molecular orbital calculations show that the LUMO of the bipyridine phosphonated ligands is at higher energy than the corresponding dicarboxylate complexes and that the thiocyanato ligands are not simple spectator ligands, whose role is to enrich electron density on the ruthenium, but are also involved in transitions from PiRu-NCS to Pibpy that extend the absorbance of the dye in the low energy part of the absorption spectrum. The photoaction spectra recorded in a sandwich regenerative photovoltaic cell indicate that the cyano and thiocyanato complexes containing the bipyridine substituted in 4,4' positions exhibit a 90-95% photoconversion efficiency on the MLCT band, whereas those containing the bipyridine substituted in 5,5' positions display lower efficiency (60-65%). The most efficient complex in the series is cis-RuL(2)(NCS)(2); however, its overall efficiency is about 30% lower than the analogue cis-Ru(H(2)dcb)(2)(NCS)(2) (H(2)dcb = 2,2'-bipyridine-4,4'-dicarboxylic acid) due to a lower absorbance in the red part of the visible spectrum.

Journal Article↗