scholarly journals Three-dimensional structure of a thermophilic family GH11 xylanase fromThermobifida fusca

2012 ◽  
Vol 68 (2) ◽  
pp. 141-144 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Suzie Otani ◽  
Esben P. Friis ◽  
Keith S. Wilson ◽  
Gideon J. Davies
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
Amino Acid Sequence Level ◽  
Thermostable Enzymes ◽  
Solvent Interactions ◽  
Three Dimensional Structure ◽  
The Family ◽  
Moderate Thermophile

Thermostable enzymes employ various structural features dictated at the amino-acid sequence level that allow them to maintain their integrity at higher temperatures. Many hypotheses as to the nature of thermal stability have been proposed, including optimized core hydrophobicity and an increase in charged surface residues to enhance polar solvent interactions for solubility. Here, the three-dimensional structure of the family GH11 xylanase from the moderate thermophileThermobifida fuscain its trapped covalent glycosyl-enzyme intermediate complex is presented. Interactions with the bound ligand show fewer direct hydrogen bonds from ligand to protein than observed in previous complexes from other species and imply that binding of the xylan substrate involves several water-mediated hydrogen bonds.

Influence of Cl/Br substitution on the stereochemical peculiarities of copper(I) π-complexes with the 1-allyl-2-aminopyridinium cation

2003 ◽  
Vol 59 (11) ◽  
pp. m478-m481 ◽  
Author(s):  
Evgeny Goreshnik ◽  
Dieter Schollmeier ◽  
Marian Mys'kiv
Keyword(s):  
Hydrogen Bonds ◽  
Electrochemical Synthesis ◽  
Three Dimensional ◽  
Alternating Current ◽  
Dimensional Structure ◽  
Three Dimensional Structure

By using alternating-current electrochemical synthesis, crystals of the CuI π-complexes bis(1-allyl-2-aminopyridinium) di-μ-chloro-bis[chlorocopper(I)], (C8H11N2)2[Cu2Cl4] or [H2NC5H4NC3H5][CuCl2], and bis(1-allyl-2-aminopyridinium) di-μ-(chloro/bromo)-bis[(chloro/bromo)copper(I)], (C8H11N2)2[Cu2Br2.2Cl1.8] or [H2NC5H4NC3H5][CuBr1.10Cl0.90], have been obtained and structurally investigated. In each of the isostructural (isomorphous) compounds, the distorted tetrahedral Cu environment involves three halide atoms and the C=C bond of the ligand. Both compounds reside on inversion centres, and the dimeric [Cu2 X 4·2H2NC5H4NC3H5] units are bonded into a three-dimensional structure by N—H...X hydrogen bonds. The Br content in the terminal X1 position is much higher than that in the bridged X2 site.

scholarly journals Crystal structure of 3-deoxy-3-nitromethyl-1,2;5,6-di-O-isopropylidene-α-D-allofuranose

2016 ◽  
Vol 72 (3) ◽  
pp. 314-317
Author(s):  
Jevgeņija Lugiņina ◽  
Vitālijs Rjabovs ◽  
Dmitrijs Stepanovs
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Compound C

The title compound, C13H21NO7{systematic name: (3aR,5S,6R,6aR)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-dimethyl-6-(nitromethyl)tetrahydrofuro[2,3-d][1,3]dioxole}, consists of a substituted 2,2-dimethyltetrahydrofuro[2,3-d][1,3]dioxolane skeleton. The furanose ringAadopts aoT4conformation. The fused dioxolane ringBand the substituent dioxolane ringCalso have twisted conformations. There are no strong hydrogen bonds in the crystal structure: only weak C—H...O contacts are present, which link the molecules to form a three-dimensional structure.

scholarly journals {(3S,5R)-5-(2,4-Difluorophenyl)-5-[(1H-1,2,4-triazol-1-yl)methyl]tetrahydrofuran-3-yl}methyl 4-methylbenzenesulfonate

IUCrData ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Qing-Shuang Ma ◽  
Xiao-Guang Wang ◽  
Lei Xu ◽  
Sun Bin ◽  
Dao-Hong Xia ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Axis Direction ◽  
Envelope Conformation ◽  
Compound C ◽  
Best Fit

In the title compound, C21H21F2N3O4S, the tetrahydrofuran ring adopts an envelope conformation with the β-C atom positioned at the flap. The triazole, difluorophenyl and tolyl rings of the various substituents on the tetrahydrofuran ring are inclined at 77.88 (12), 83.81 (10) and 81.00 (10)°, respectively, to the best-fit mean plane through the five atoms of the tetrahydrofuran ring. In the crystal, weak C—H...O and C—H...F hydrogen bonds link the molecules into a three-dimensional structure, with molecules stacked along thea-axis direction.

scholarly journals (E)-N′-[4-(Dimethylamino)benzylidene]propionohydrazide monohydrate

IUCrData ◽  
2016 ◽  
Vol 1 (10) ◽  
Author(s):  
S. Naveen ◽  
Seranthimata Samshuddin ◽  
Manuel Rodrigues ◽  
Dandavathi Arunkumar ◽  
N. K. Lokanath ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Crystal Water ◽  
Three Dimensional Structure ◽  
Π Interactions ◽  
Compound C

In the title hydrated hydrazine compound, C12H17N3O·H2O, the C=N bond adopts an E conformation. In the crystal, water molecules bridge the hydrazine molecules, via N—H...O and O—H...O hydrogen bonds, forming sheets parallel to the bc plane. There are C—H...π interactions present within the sheets, and further C—H...π interactions link the sheets to form a three-dimensional structure.

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

Zona Pellucida Proteins, Fibrils, and Matrix

2020 ◽  
Vol 89 (1) ◽  
pp. 695-715
Author(s):  
Eveline S. Litscher ◽  
Paul M. Wassarman
Keyword(s):  
Extracellular Matrix ◽  
Zona Pellucida ◽  
Three Dimensional ◽  
Structural Features ◽  
Biological Properties ◽  
Preimplantation Development ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Early Embryos ◽  
N Terminus

The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1–4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2–ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.

scholarly journals Crystal structure of tris(2,2′-bipyridine)cobalt(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide)

2019 ◽  
Vol 75 (2) ◽  
pp. 142-145
Author(s):  
Jamila Benabdallah ◽  
Zouaoui Setifi ◽  
Fatima Setifi ◽  
Habib Boughzala ◽  
Abderrahim Titi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Distorted Octahedron ◽  
Dimensional Structure ◽  
Cobalt Ion ◽  
Space Group ◽  
Three Dimensional Structure ◽  
Rotation Axes

In the title compound, [Co(C10H8N2)3](C9H5N4O)2, the tris(2,2′-bipyridine)cobalt(II) dication lies across a twofold rotation axes in the space group C2/c. The N atoms of the three bipyridine ligands form a distorted octahedron around the cobalt ion. All the N atoms of the polynitrile 1,1,3,3-tetracyano-2-ethoxypropenide anions participate in C—H...N hydrogen bonds ensuring crystal cohesion and forming a three-dimensional structure. The structure is further stabilized by C—H...π(cation) and anion...π(cation) interactions.

scholarly journals Four classes of β-hairpins in proteins

1986 ◽  
Vol 240 (1) ◽  
pp. 289-292 ◽  
Author(s):  
E J Milner-White ◽  
R Poet
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Frequency Of Occurrence ◽  
Single Class ◽  
Three Dimensional Structure ◽  
Beta Hairpins ◽  
Beta Hairpin

We show that beta-hairpins can be divided into four classes, each with a number of members. Hairpins from a single class are readily interconverted by loss or gain of hydrogen bonds, but interconversion between classes requires complete unzipping and reformation of the entire beta-hairpin. Sibanda & Thornton [(1985) Nature (London) 316, 170-174] have classified beta-hairpins as either two-residue, three-residue, four-residue etc., loops. We point out that their nomenclature, by itself, gives rise to ambiguities, but that, if the class (one of the four mentioned above) is also specified, the description of beta-hairpins becomes straightforward. A range of proteins of known three-dimensional structure has been examined; it provides examples of hairpins of each of the four classes and give some indication of their frequency of occurrence. The distribution observed is substantially different from that described by Sibanda & Thornton [(1985) Nature (London) 316, 170-174].

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