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1.
The title compound has been found to consist of tricapped trigonal prismatic Sm(H2O)93+ ions in C2v symmetry, sandwiched between expanded ‘close packed’ layers of bromide ions, with 1,4-dioxan molecules in chair conformation hydrogen bonding between the equatorial water molecules of adjacent cations.Orthorhombic, Amm2, a = 8.010(3), b = 19.848(4), c = 7.388(3) Å, R = 0.022 for 992 unique reflexions.  相似文献   

2.
3.
The biosynthesis of UDP-N-acetylmuramic acid (UDP-MurNAc) by reduction of UDP-N-acetylglucosamine-enolpyruvate (UDP-GlcNAc-EP) in an NADPH and FAD-dependent reaction in bacteria is one of the key steps in peptidoglycan biosynthesis catalyzed by UDP-N-acetylglucosamine-enolpyruvate reductase (MurB). Here, we present the crystal structure of Mycobacterium tuberculosis MurB (MtbMurB) with FAD as the prosthetic group at 2.0 Å resolution. There are six molecules in asymmetric unit in the form of dimers. Each protomer can be subdivided into three domains and the prosthetic group, FAD is bound in the active site between domain I and domain II. Comparison of MtbMurB structure with the structures of the Escherichia coli MurB (in complex with UDP-GlcNAc-EP) and Pseudomonas aeruginosa MurB (in complex with NADPH) showed all three structures share similar domain architecture and residues in the active site. The nicotinamide and the enol pyruvyl moieties are well aligned upon superimposition, both positioned in suitable position for hydride transfer to and from FAD. The comparison studies and MD simulations demonstrate that the two lobes of domain-III become more flexible. The substrates (NADPH and UDP-GlcNAc-EP) binding responsible for open conformation of MurB, suggesting that NADPH and UDP-GlcNAc-EP interactions are conformationally stable. Our findings provide a detail mechanism about the closed to open state by binding of NADPH and UDP-GlcNAc-EP induces the conformational changes of MurB structure that may trigger the MurB catalytic reaction.  相似文献   

4.
Abstract

The title compound, 9-[4-hydroxy-2-(hydroxymethyl)-butyl]guanine (2HM-HBG), crystallizes in the triclinic space group P1 with two independent molecules and one water molecule in the asymmetric unit. The acyclic chain of one molecule is in the fully extended form, and the other partially folded. The orientation of this chain with respect to the base corresponds to the conformation syn in natural nucleosides. The conformations of the two molecules were compared with the solution conformation from an analysis of the 1H-1H vicinal coupling constants. The comportment of some acyclonucleosides in several enzyme systems is examined in relation to their existence in folded or extended forms.  相似文献   

5.
Interaction between l-arabinose and the zinc group metal-ion salts has been studied in aqueous solution and solid complexes of the type M(l-arabinose)X2·nH2O, where M = Zn(II), Cd(II), and Hg(II) ions, X = Cl or Br, and n = 0–2 have been isolated and characterized. On comparison with the structurally known Ca(l-arabinose) Cl2·4H2O and the corresponding magnesium compounds, it is concluded that the Zn(II) and Cd(II) ions are six-coordinated, binding to two arabinose moieties via 03, 04 of the first and 01, 05 of the second sugar molecule as well as to two H2O molecules. The Hg(II) ion binds only to two sugar molecules in a similar fashion to zinc and cadmium ions, resulting in a four coordination around the mercury ion. The strong intermolecular hydrogen bonding network of the free arabinose is rearranged to that of the sugar OH...H2O...halide system upon metalation. The β-anomer sugar conformation is predominant in the free sugar, while the α-anomer conformation is preferred by the alkaline earth and Zn(II), Cd(II), and Hg(II) cations.  相似文献   

6.
The crystal and molecular structures of Th(oda)2(H2O)4·6H2O (1) and Na2[Th(oda)3]·2NaNO3 (2) (oda = oxydiacetate) have been determined from three-dimensional X-ray diffraction data and refined by least squares to R = 0.049 and Rw = 0.049 for 2265 independent reflections for (1) and to R = 0.024 and Rw = 0.023 for 2196 independent reflections for (2).Crystal parameters are as follows: (1), tetragonal, space group P41212, a = 10.335(2), c = 20.709(5) Å and Z = 4; (2), monoclinic, space group C2/c, a = 17.096(5), b = 9.451(2), c = 16.245(4) Å, β = 107.8(1) and Z = 4.In both compounds the thorium atom lies on a crystallographic two-fold axis. The co-ordination number for thorium in (1) is 10 (bicapped square antiprism geometry), the compound is monomeric, the two oda ligands are tridentate to the metal, and four water molecules complete the coordination sphere; in thorium (2) the coordination number is 9 (tricapped trigonal prism geometry) with three oda ligands tridentate to the metal, the [Th(oda)3]2? and NO3? anions are held together through the sodium ions which are coordinated both to the oda carboxylic oxygens and to the nitrate oxygens.The ThO coordination distances are: in (1) 2.411(8), 2.414(9) for the carboxylic oxygens, 2.479(10) and 2.486(8) for water molecules and 2.697(9) for the etheric oxygen and in (2) 2.384(3), 2.402(4) and 2.402(4) for the carboxylic oxygens, 2.559(5) and 2.562(4) Å for the etheric oxygens.  相似文献   

7.
《Inorganica chimica acta》1987,129(2):199-204
Condensation reactions of three isomers of bis(diethylenetriamine)cobalt(III) with formaldehyde and ammonia were studied. The s-fac isomer gave a main product containing two molecules of the cyclic amine, 1,3,5,8-tetraazacyclodecane. It was unstable in acidic solution to give several decomposition products. The encapsulated complex in which all the nitrogens were attacked by formaldehyde could not be obtained. The main product of the u-fac isomer was a half encapsulated complex, i.e., three of the four primary amino groups reacted with formaldehyde and ammonia to produce a cobalt(III) complex of 3-(7-amino-2,5-diazaheptyl)-1,3,5,8-tetraazacyclodecane. The mer isomer gave a complex of 1,4,7,9,11,14,17-heptaazaheptadecane, together with the same reaction product as the one from the u-fac isomer.  相似文献   

8.
In plants, the ureide pathway is a metabolic route that converts the ring nitrogen atoms of purine into ammonia via sequential enzymatic reactions, playing an important role in nitrogen recovery. In the final step of the pathway, (S)-ureidoglycolate amidohydrolase (UAH) catalyzes the conversion of (S)-ureidoglycolate into glyoxylate and releases two molecules of ammonia as by-products. UAH is homologous in structure and sequence with allantoate amidohydrolase (AAH), an upstream enzyme in the pathway with a similar function as that of an amidase but with a different substrate. Both enzymes exhibit strict substrate specificity and catalyze reactions in a concerted manner, resulting in purine degradation. Here, we report three crystal structures of Arabidopsis thaliana UAH (bound with substrate, reaction intermediate, and product) and a structure of Escherichia coli AAH complexed with allantoate. Structural analyses of UAH revealed a distinct binding mode for each ligand in a bimetal reaction center with the active site in a closed conformation. The ligand directly participates in the coordination shell of two metal ions and is stabilized by the surrounding residues. In contrast, AAH, which exhibits a substrate-binding site similar to that of UAH, requires a larger active site due to the additional ureido group in allantoate. Structural analyses and mutagenesis revealed that both enzymes undergo an open-to-closed conformational transition in response to ligand binding and that the active-site size and the interaction environment in UAH and AAH are determinants of the substrate specificities of these two structurally homologous enzymes.  相似文献   

9.
Crystal structure of peptide cyclo-(D-Val-L-Pro-L-Val-D-Pro)   总被引:1,自引:0,他引:1  
The crystal and molecular structure of the rubidium/picrate complex of the peptide cyclo-(D-val-L-pro-L-val-D-pro)3, called prolinomycin, has been determined by X-ray crystallography and found to be similar to the well known ion-carrier valinomycin. Prolinomycin crystallizes in the triclinic system with two prolinomycin molecules and two each rubidium cations and picrate anions in the unit cell. There are also ordered toluene and chloroform molecules, which are the solvents of crystallization, in the unit cell. The conformation of the two crystallographically independent prolinomycin molecules in the unit cell are very similar. Potential energy calculations show that the cation is bound more strongly in prolinomycin compared to valinomycin. This was also observed in solution (7).  相似文献   

10.
The modification of RNA nucleotide bases, a fundamental process in all cells, alters the chemical and physical properties of RNA molecules and broadly impacts the physiological properties of cells. tRNA molecules are by far the most diverse-modified RNA species within cells, containing as a group >80% of the known 96 chemically unique nucleic acid modifications. The greatest varieties of modifications are located on residue 37 and play a role in ensuring fidelity and efficiency of protein synthesis. The enzyme dimethylallyl (Delta(2)-isopentenyl) diphosphate:tRNA transferase catalyzes the addition of a dimethylallyl group to the exocyclic amine nitrogen (N6) of A(37) in several tRNA species. Using a 17 residue oligoribonucleotide corresponding to the anticodon arm of Escherichia coli tRNA(Phe), we have investigated the structural and dynamic changes introduced by the dimethylallyl group. The unmodified RNA molecule adopts stem-loop conformation composed of seven base-pairs and a compact three nucleotide loop. This conformation is distinctly different from the U-turn motif that characterizes the anticodon arm in the X-ray crystal structure of the fully modified yeast tRNA(Phe). The adoption of the tri-nucleotide loop by the purine-rich unmodified tRNA(Phe) anticodon arm suggests that other anticodon sequences, especially those containing pyrimidine bases, also may favor a tri-loop conformation. Introduction of the dimethylallyl modification increases the mobility of nucleotides of the loop region but does not dramatically alter the RNA conformation. The dimethylallyl modification may enhance ribosome binding through multiple mechanisms including destabilization of the closed anticodon loop and stabilization of the codon-anticodon helix.  相似文献   

11.
M. Suwalsky  A. Llanos 《Biopolymers》1977,16(2):403-413
A structural study of the synthetic polypeptide poly(L -lysine hydrobromide) has been made by X-ray fiber techniques. The investigation was undertaken to determine whelther this polymer undergoes conformational transitions as a function of hydration in a manner similar to other chemically related basic polypeptides. Specifically, a comparison with the previously reported structures of the hydrochloride form of poly(L -lysine) was sought. Homogeneous powder mixtures with various amounts of water and oriented fibers of poly(L -lysine hydrobromide) at different relative humidities were X-ray photographed. Reversible transitions amorphous state ? β-pleated sheet ? α-helix ? isotropic solution as a function of increasing/decreasing degrees of hydration were found. The β-pleated-sheet conformation was observed between 33% and 76% relative humidities (containing about one and three molecules of water per residue, respectively). Each pleated sheet was formed by “antiparallel” chains, and the sheets were piled up along the b-axis. The spacings of this conformation did not vary appreciably with hydration. The observed reflections at 52% relative humidity (1.4 molecules of water per residue) could be indexed satisfactorily in terms of an orthorhombic unit cell, of space group P21221, with a = 9.52 Å, b = 16.44 Å, and c = 6.80 Å. These dimensions were shown by models to be compatible with the proposed structure. The α-helix conformation was present in specimens photographed at 76% relative humidity and up, and containing between three and fifteen molecules of water per residue. The helices were packed parallel to each other in a hexagonal array but randomly along or about their lengths. Increasing the hydration from five to fifteen molecules of water per residue causes the a-axis to increase from 16.9 to 20.8 Å. Twenty molecules of water per residue produced an isotropic solution. Despite some structural differences between the hydrobromide and hydrochloride forms it is concluded that the role played by the anions is mainly related to determining the water content levels at which conformational changes occur. Therefore, the anions do not significantly influence the prevailing conformation in this particular system, but might affect the packing arrangement of the polypeptide chains.  相似文献   

12.
The structure of the tin(III) complex [Sn2(CH2CH2CN)6] has been determined. There are two independent molecules in the crystal, both adopt distorted eclipsed conformation. The molecular and electronic structures of this compound have been studied both at the semiempirical level and with the use of non-empirical ab initio methods. The calculated Sn–Sn distances agree well with those found crystallographically. The results of calculations showed that the eclipsed conformation of complex is more stable as compared with staggered conformation. The compound show modest cytotoxic activity against A549 and HSMC cells.  相似文献   

13.
The crystal structure of isothiocyanatotriphenyl- (pyridinium-2-carboxylato)tin(IV) monohydrate is reported. The crystals are monoclinic, space group P21/n, a = 10.349(2), b =12.003(2), c = 19.325(4) Å, β = 97.68(2)°, Z = 4, refined to RF = 0.024 on 4249 observed reflections.The tin(IV) atom is five-coordinate, being bound to three phenyl groups, the isothiocyanato nitrogen atom and an oxygen from the picolinic acid. The geometry around the tin atom is trigonal bipyramidal, with the three phenyl groups occupying the equatorial positions, while the picolinic acid oxygen and the isothiocyanato nitrogen are coordinated axially. The acidic proton of picolinic acid has shifted position in the complex, and is bound to the heterocyclic nitrogen atom. The acid is thus coordinated in the form of a zwitterion. These trigonal bipyramidal units are linked together as dimers by pairs of water molecules, each of which hydrogen- bonds to the non-coordinated carboxylate oxygen atoms of both picolinic acid molecules, plus the heterocyclic nitrogen atom of one picolinic acid molecule. For complex formation with the protonated acid, theheterocyclic nitrogen should be alpha to the carboxylic acid group.  相似文献   

14.
The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and their structures were solved by direct methods. Least-squares refinement produced final R-factors of 0.027 for the 2'-F-dd-araA structure and of 0.044 for the 2'-F-dd-aral structure, respectively. The latter structure contains a two-fold disordered conformation of the sugar moiety. All three conformers (one for 2'-F-dd-araA and two for 2'-F-dd-aral) adopt an anti chi CN glycosyl torsion angle. The sugar in the 2'-F-dd-araA structure has a C2'-endo pucker conformation, whereas the sugar in the 2'-F-dd-aral structure has a mixture of C2'-endo and C3'-endo pucker conformations. When the sugar adopts the C2'-endo conformation, the torsion angle about the C4'-C5' bond is in a transgauche+ conformation. In contrast, when the sugar adopts the C3'-endo conformation, the torsion angle about the C4'-C5' bond is in a gauche(+)-gauche- conformation. The C2'-F bond distance is 1.406(3) A, similar to that found in other aliphatic C-F bonds. The results suggest that the 2'-fluoro-2',3'-dideoxyarabinosyl nucleosides do not have a strong preference for either C2'-endo or C3'-endo sugar pucker.  相似文献   

15.
Structures of (Pro‐Pro‐Gly)4‐Xaa‐Yaa‐Gly‐(Pro‐Pro‐Gly)4 (ppg9‐XYG) where (Xaa, Yaa) = (Pro, Hyp), (Hyp, Pro) or (Hyp, Hyp) were analyzed at high resolution using synchrotron radiation. Molecular and crystal structures of these peptides are very similar to those of the (Pro‐Pro‐Gly)9 peptide. The results obtained in this study, together with those obtained from related compounds, indicated the puckering propensity of the Hyp in the X position: (1) Hyp(X) residues involved in the Hyp(X):Pro(Y) stacking pairs prefer the down‐puckering conformation, as in ppg9‐OPG, and ppg9‐OOG; (2) Hyp(X) residues involved in the Hyp(X):Hyp(Y) stacking pairs prefer the up‐puckering conformation if there is no specific reason to adopt the down‐puckering conformation. Water molecules in these peptide crystals are classified into two groups, the 1st and 2nd hydration waters. Water molecules in the 1st hydration group have direct hydrogen bonds with peptide oxygen atoms, whereas those in the 2nd hydration group do not. Compared with globular proteins, the number of water molecules in the 2nd hydration shell of the ppg9‐XYG peptides is very large, likely due to the unique rod‐like molecular structure of collagen model peptides. In the collagen helix, the amino acid residues in the X and Y positions must protrude outside of the triple helix, which forces even the hydrophobic side chains, such as Pro, to be exposed to the surrounding water molecules. Therefore, most of the waters in the 2nd hydration shell are covering hydrophobic Pro side chains by forming clathrate structures. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 361–372, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com  相似文献   

16.
Anomerically free acidic xylo-oligosaccharides have shown interesting biological properties when tested against Gram-positive and Gram-negative aerobically grown bacteria, as well as against Helicobacter pylori, sarcoma-180 and other tumors. We report here a structure–activity relationship study on the role of 4-O-methyl glucuronic acid (MeGlcUA) in regulating aggregation of β-polyxylosides of (9H-fluoren-9-yl)- methanol obtained via the action of Thermotoga neapolitana xylanase. Neutral compounds from mono- to penta-β-1,4 xylosides were obtained from this biocatalyzed reaction. In addition, acidic components among products, carrying an α-1,2 4-O-methyl glucuronic acid (MeGlcUA) were also isolated. An anti-proliferative test of these compounds on human epithelial EFO 27 ovarian cancer cells indicated that the presence of MeGlcUA modulates their biological activity, while its absence induces molecular aggregation. The three-dimensional structure of the most active MeGlcUA β-polyxyloside was investigated by resorting to NOESY experiments supported by dynamic force-field calculations with/without constraints. The 3D structure is characterized by all sugars possessing a 4C1 chair conformation. The MeGlcUA moiety, and the external and middle xyloses adopt a hairpin-shaped conformation, generating a non-planar arrangement of the molecule with the aromatic ring folding back toward the carbohydrate chain. Such a non-planar conformation may justify the lack of aggregation.  相似文献   

17.
The crystal structure of chlorotriphenyl(quinolinium-2-carboxylato)tin(IV) monohydrate is reported. The crystals are monoclinic, space group C2/c with cell parameters a = 20.048(3) Å, b = 11.724(1) Å, c = 23.291(3) Å, ]gb = 113.42(1), Z = 8, refined to RF = 0.034 on 3331 observed reflections. The tin(IV) atom is five-coordinate, being found to three phenyl groups, the chlorine atom and an oxygen from the quinaldic acid. The geometry around the tin atom is trigonal bipyramidal, with the three phenyl groups occupying the equatorial positions, and the chlorine and quinaldic acid oxygen, the apical ones. The acidic proton of quinaldic acid has shifted position in the complex, and is bound to the heterocyclic nitrogen atom.The acid is thus coordinated in the form of a zwitterion. These trigonal bipyramidal units are linked together as dimers by pairs of water molecules, each of which hydrogen-bonds to the non-coordinated carboxylate oxygen atoms of both quinaldic acid molecules, plus the heterocyclic nitrogen atom of one quinaldic acid molecule. For complex formation with the protonated acid, the heterocyclic nitrogen should be alpha to the carboxylic acid group.  相似文献   

18.
Abstract

The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P212121 with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)Å, V = 5884 (3) Å3, Z = 8, R = 0.086. VALa crystallises in space group P21 with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) Å, β = 95.84 (8)°, V = 3040(4) Å3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel β-sheet arrangement in both the structures. Several of the Cα hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand.

An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and αL conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed αR conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.  相似文献   

19.
The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2(1),2(1),2(1), with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)A. V = 5,884 (3) A3, Z = 8, R = 0.086. VALa crystallises in space group P2(1) with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) A, beta = 95.84 (8) degrees , V = 3,040(4) A3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel beta-sheet arrangement in both the structures. Several of the Calpha hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand. An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and alphaL conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed alphaR conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.  相似文献   

20.
The structure of the complex [Pt(trans-1,2-di- aminocyclohexane) (acetate)2]·H2O has been determined by X-ray diffraction. This racemic compound is orthorhombic, space group Aba2, a = 20.813(9), b = 7.926(5), c = 17.296(8) Å, Z = 8. The structure was refined on 1214 nonzero Cu Kα reflections to R = 0.028. The square planar environment of Pt includes the amino groups of the diamine in cis positions and oxygens from two monodentate acetates. The PtN and PtO distances average 2.00(3) and 2.02(3) Å, respectively. The bite of the diamine ligand imposes a NPtN angle of 85(1)°, whereas the small OPtO angle of 85(1)° probably results from packing effects. The average plane through the puckered cyclohexyl ring makes an angle of 19° with the PtN2O2 plane. The molecules are stacked by pairs along the b axis. The two molecules of each pair are 180° apart about the stacking axis, and form altogether four NH···O hydrogen bonds.  相似文献   

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