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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    ISSN: 1573-6881
    Keywords: Cytochrome c oxidase ; membrane protein ; proton pump ; O2 reduction ; x-ray crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract Thirteen different polypeptide subunits, each in one copy, five phosphatidyl ethanolamines and three phosphatidyl glycerols, two hemes A, three Cu ions, one Mg ion, and one Zn ion are detectable in the crystal structure of bovine heart cytochrome c oxidase in the fully oxidized form at 2.8 Å resolution. A propionate of hems a, a peptide unit (–CO–NH–), and an imidazole bound to CuA are hydrogen-bonded sequentially, giving a facile electron transfer path from CuA to heme a. The O2 binding and reduction site, heme a 3, is 4.7 Å apart from CuB. Two possible proton transfer paths from the matrix side to the cytosolic side are located in subunit I, including hydrogen bonds and internal cavities likely to contain randomly oriented water molecules. Neither path includes the O2 reduction site. The O2 reduction site has a proton transfer path from the matrix side possibly for protons for producing water. The coordination geometry of CuB and the location of Tyr244 in subunit I at the end of the scalar proton path suggests a hydroperoxo species as the two electron reduced intermediate in the O2 reduction process.
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  • 2
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 365-370 
    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] SCFFbs1 is a ubiquitin ligase that functions in the endoplasmic reticulum (ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins, recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose). Here we report the ...
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  • 3
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 1535-1544 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The (Fe2S2)2+ complex of an artificial 20-peptide ligand, Ac-Pro-Tyr-Ser-Cys-Arg-Ala-Gly-Ala-Cys-Ser-Thr-Cys-Ala-Gly-Pro-Leu-Leu-Thr-Cys-Val-NH2, containing an invariant Cys-A-B-C-D-Cys-X-Y-Cys (A, B, C, D, X, Y = amino acid residues) fragment of plant-type ferredoxins was synthesized by a ligand exchange method with [Fe2S2(S-t-Bu)4]2-. 1H-nmr spectroscopic and electrochemical data of the complex indicate the presence of two coordination isomers. One of them having a Cys-X-Y-Cys bridging coordination to the two Fe(III) ions, has the (Fe2S2)2+ core environment similar to those of the denatured plant-type ferredoxins and exhibits a positive shifted redox potential at -0.64 V vs saturated colonel electrode (SCE) in N,N-dimethylformamide (DMF). Another isomer with the Cys-A-B-C-D-Cys bridging coordination shows a negative redox potential at -0.96 V vs SCE in DMF. © 1992 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 286 (1980), S. 33-39 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] X-ray diffraction studies reveal that the polypeptide chain of the southern bean mosaic virus protein subunit has a fold closely similar to the shell domain of tomato bushy stunt virus. The protruding domain of tomato bushy stunt virus is absent in southern bean mosaic virus. The tertiary structure ...
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  • 5
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 286 (1980), S. 522-524 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] We will give only a brief description of our study, because full details of the analytical procedures and crystal structure of ferredoxin will be reported elsewhere. The crystals were orthorhombic with a space group C2221 of a = 62.32, b = 28.51, c = 108.08 and Z = 8. Intensity data, including ...
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  • 6
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 529-535 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two azide ions were identified, one between the Fe and Cu atoms in the O2-reduction site and the other at the transmembrane surface of the enzyme, in the crystal structure of the azide-bound form of bovine heart cytochrome c oxidase at 2.9 Å resolution. Two geometries, a μ-1,3 type geometry between the Fe and Cu atoms and a terminal geometry on the Fe atom, are equally possible for an azide ion in the O2-reduction site. The other azide molecule was hydrogen bonded to an amide group of an asparagine and a hydroxyl group of tyrosine in a μ-1,1 type geometry. The antisymmetric infrared bands arising from these azide ions, which show essentially identical intensity [Yoshikawa & Caughey (1992), J. Biol. Chem. 267, 9757–9766], strongly suggest terminal binding of the azide to Fe. The electron density of all three imidazole ligands to CuB was clearly seen in the electron-density map of the azide-bound form of bovine heart enzyme, in contrast to the crystal structure of the azide-bound form of the bacterial enzyme [Iwata et al. (1995), Nature (London), 376, 660–669], which lacks one of the three imidazole ligands to CuB.
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  • 7
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 80-81 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The bond energy constant of methionine Sδ—Cε, 170.066 kcal mol−1 Å−2, is given as a default value in X-ray protein structure refinement with X-PLOR [Brünger (1992). X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. New York University Press]. When the atomic parameters of 3564 amino acid residues of bovine heart cytochrome c oxidase were refined at 2.0 Å resolution by using X-PLOR with default restraining parameters, 36 bond lengths deviated by over 0.06 Å from their ideal values. Out of the 36 bonds, 25 were methionine Sδ—Cε bonds. Refinement with an energy parameter of 500.0 kcal mol−1 Å−2 for the methionine Sδ—Cε bond resulted in convergence of the Sδ—Cε bond lengths to within 0.06 Å from their ideal values and reduced the crystallographic R and free-R factors by 0.6 and 0.3%, respectively. Consequently, a strong bond energy constant for Sδ—Cε of 500.0 kcal mol−1 Å−2 is recommended instead of the default value of 170.066 kcal mol−1 Å−2.
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  • 8
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 941-947 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of bovine heart cytochrome c oxidase solved for orthorhombic crystals showed a dimeric structure stabilized by four subunit–subunit contacts, namely, subunit Vb–subunit Vb on the matrix side, subunit I–subunit VIa, subunit VIa–subunit I in the transmembrane region and subunit VIb–subunit VIb on the intermembrane side. The same intermonomer contacts as in the orthorhombic crystals were observed in both hexagonal and tetragonal crystals, the X-ray structures of which were determined by the molecular-replacement method. These results suggest that the dimeric structure also exists under physiological conditions. These contacts, especially the subunit IVa–subunit I contact, in which the N-terminal portion of subunit IVa is placed on the surface of subunit I near the dioxygen-reduction site, indicate that the function of the bovine heart enzyme is likely to be controlled by perturbation of the monomer–monomer association.
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  • 9
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 77-84 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Rice dwarf virus crystals belong to space group I222 with cell parameters a = 770 (2), b = 795 (5), c = 814 (5) Å and α = β = γ = 90°. The unit cell of the crystal contains two viruses at the origin and body-centred positions. Using data synthesized from a rice dwarf virus model crystal in the space group I222, the possibility of ab initio phasing was thoroughly examined. The centric nature of the initial phases was unexpectedly broken by extensive iteration of the non-crystallographic symmetry averaging. The structure of rice dwarf virus was then solved with ab initio phasing up to 20 Å resolution. The triangulation number determined by the present study is T = 13, which is different from the triangulation number, T = 9, previously determined by electron microscopy [Uyeda & Shikata (1982). Ann. Phytopathol. Soc. Jpn, 48, 295–300].
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  • 10
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 210-211 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The β-carbonic anhydrase from the red alga Porphyridium purpureum was heterologously expressed, purified and crystallized. The crystals belong to space group P21 (unit-cell parameters a = 63.8, b = 113.9, c = 73.8 Å, β = 104.1°) with two subunits per asymmetric unit and diffract to 2.5 Å resolution.
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