Wolfram Saenger

Crystal and molecular structure of cyclohepta-amylose dodecahydrate ☆

Abstract β-Cyclodextrin (cyclohepta-amylose, β-CD) is a torus-shaped, cyclic heptasaccharide consisting of (1→4)-linked α- d -glucopyranosyl residues. It is able to form inclusion complexes with small molecules in aqueous solution because of its annular aperture (width, 6.2 A). β-Cyclodextrin dodecahydrate, the “empty” β-CD, crystallises from water in space group P21, with cell constants a = 21.29(2), b = 10.33(1), c = 15.10(2) A, and β = 112.3(5)°. A total of 5189 X-ray counter-data were collected on a four-circle diffractometer. The crystal structure was solved on the basis of the highly isomorphous β-CD · 2HI · 8H2O adduct, and the atomic parameters were refined by the full matrix, least-squares method to R = 7.3% for all data. The crystal structure belongs to the cage type. The β-CD macrocycle exists in an open, circular conformation stabilised by intramolecular hydrogen-bonds between HO-2 and HO-3 of adjacent glucosyl residues; four of the seven HO-6 groups are in the favoured (−)gauche orientation with respect to O-5, two are in the (+)gauche orientation, and one is disordered over these two orientations. The 6.5 water molecules within the cavity are distributed over 8 sites and display extensive thermal motion which is probably correlated with statistical disorder.

“Induced-fit”-type complex formation of the model enzyme α-cyclodextrin

Abstract On the basis of X-ray and neutron data for several α-cyclodextrin·substrate complexes it is shown that basically two different structures for α-cyclodextrin exist, one “tense”, the other “relaxed”. An “induced-fit”-like mechanism for α-cyclodextrin complex formation is proposed.

A Pyrimidine nucleoside in the syn conformation: Molecular and crystal structure of 4-thiouridine-hydrate

Abstract 4-Thiouridine is a constituent of several transfer RNAs. Four molecules of this nucleoside crystallize together with six water molecules in a unit cell of the monoclinic space group C 2. The structure of 4-thiouridine was solved from three-dimensional X-ray data using the heavy-atom technique. Atomic distances but not the angles within the molecule are in the usual range, the heterocyclic system assuming a keto-keto structure and the ribose moiety arranged in a C(3′)- endo conformation. Most striking is the fact that 4-thiouridine is the first pyrimidine nucleoside to be found in the syn conformation. The crystal packing is such that the pyrimidine rings form endless stacks in the a-b plane, paralleled by continuous chains of ribose residues and water molecules. Some thoughts on the definition of the torsion angle about the glycosidic bond are expressed in the Appendix.

A structural model for the polyadenylic acid single helix.

Abstract In the crystal, the poly(A) fragment ApApA assumes a conformation with the 5′-terminal and middle adenosines in a single helical arrangement. From the atomic co-ordinates of these two nucleotides the structure of the poly(A) single helix was derived mathematically. The helix has a pitch height of 25.4 A, nine nucleotides per turn and the normals to the adenine bases form an angle of 66 ° with the helix axis.

Crystal structure of the γ-cyclodextrin n-propanol inclusion complex; Correlation of α-, β-, γ-cyclodextrin geometries

Abstract Crystals of the hydrated n-propanol inclusion complex of γ-cyclodextrin (γ-CD; cyclo-octaamylose) have space group P4, a = b = 23.759(7), c = 23.069(7)A and six quarter γ-CD per asymmetric unit. The structure was solved by YZARC and refined to R = 14% using 6300 X-ray counter data. The γ-CD are stacked, n-propanol (not located) occupies the channel-type cavity and 27 water sites populate interstices between stacks. Within the stacks γ-CD are arranged head-to-head as well as head-to-tail and H-bonded with O(2), O(3), O(6) hydroxyls. In the series α-,β-,γ-CD, angles C(1′)-O(4)-C(4) reduce from 119°-117.7°-112.6°, virtual O(4′)⋯O(4) distances increase 4.23-4.39-4.48 A. intramolecular H-bonding distances O(2)⋯O(3) between adjacent glucoses, 3.00 A in α-CD are wider than ∼2.83 A in β- and γ-CD, indicating a greater flexibility of the former.

Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains.

Abstract Analysis of the X-ray fibre diffraction pattern obtained from synthetic poly-2-thiouridylic acid (poly(s 2 U)), a 2-thiosubstituted homologue of polyuridylic acid, reveals that the poly(s 2 U) homopolymer exists in a structure similar to that of A -DNA: two polynucleotide chains are complexed in an antiparallel manner to form a helix with a pitch of 28.8 A and 11 base pairs per turn. The radius of the helix is 0.5 A less than that of A -DNA due to the exclusive occurrence of pyrimidine bases. A molecular model of poly(s 2 U) was derived with unsymmetric N (3) H · · · O (4) and S (2) · · · HN (3) hydrogen bonding between bases, and base pair tilt of 18 ° relative to the helix axis. The peculiar base pairing scheme implies that no symmetry relation exists between the two glycosidic C (1′) N (1) bonds or between the attached ribose-phosphate chains of a base pair. Thus two chains, α and β, are obtained which significantly differ from each other in geometry: the α-chain appears more compressed than an A -DNA polynucleotide chain, the β-chain more extended. Further, the sulphur atoms of the nucleobases within the β-chain are in contact with the glycosidic bonds of the adjacent nucleotides. The bases of the α-chain are stacked such that the base sulphur atoms are located near the N (1) atoms of adjacent bases, giving rise to continuous S · · · N, S · · · N, S · · · N interactions. Similar S · · · N stacking interactions have also been observed in a number of crystal structures of thiopyrimidine nucleosides and seem to indicate a general packing feature. These interactions might be responsible for the increased helix stability of poly(s 2 U) (melting point 68.5 °C) relative to poly(U) (melting point 8 °C under identical conditions) and for the relatively high stability of double helical polynucleotides containing 2-thiopyrimidine bases in contrast to those with 4-thiopyrimidine bases. Further, yeast tRNA 3 Glu contains a 2-thiouridine derivative in the 3′-position of its anticodon and recognizes GAA but not GAG as the codon for glutamic acid. This specificity can be explained when considering the preferred S · · · N stacking interactions which would restrict “wobbling” of the 3′-nucleotide of the anticodon.

6-Azauridine, a nucleoside with unusual ribose conformation: The molecular and crystal structure

Abstract The cytostatic analogue ribo-6-azauridine crystallizes in the orthorhombic space group P212121 with eight molecules per unit cell of dimensions a = 20.230, b = 7.709, c = 12.863 A . A trial structure was obtained by direct methods. Least-squares refinement of co-ordinates and anisotropic thermal parameters based on 1998 reflections measured on a four-circle diffractometer led to a discrepancy index R = 4.0%. Like uridine, 6-azauridine has the anti conformation about the glycosidic bond and a C(3′)-endo sugar pucker. Unlike uridine, it exhibits a close approach of N(6) to C(2′) at only 2.814 and 2.844 A in the two independent molecules, and a C(5′)(5′) bond that is gauche to C(4′)O(1′) but trans to C(4′)C(3′); this conformation about a C(4′)C(5′) bond has never been observed before for C(3′)-endo puckered riboses in the crystalline state. The crystal structure displays a pseudo-A face centering and very similar conformational parameters for the two independent molecules. Every OH and NH group in the structure serves as a proton donor in a hydrogen bond, including an unusual N(3)—H(3) … O(1′) link. Molecular orbital calculations by the extended Huckel method indicate that from uridine to 6-azauridine the net charge changes sign at ring positions 5 and 6 and disappears at 1.

Conformation of nucleosides: The comparison of an X-ray diffraction and proton nmr study of 5′,2-O-cyclo, 2′,3′-O-Isopropylidene uridine

Abstract The title compound crystallizes in the monoclinic space group P21 with unit cell dimensions, a = 9.091 A , b = 6.404 A , c = 10.395 A , β = 93.6°, and there are two molecules per unit cell. The crystal structure has been determined on the basis of 828 diffraction intensities measured with a four-circle diffractometer, Cu radiation, and refined by the method of least squares to a residual index of R = 0.049. The uracil residue shows the features typical for O(2) cyclic derivatives: the C(2)-N(3) bond length, 1.283 A, is characteristic of a double bond. The ribofuranose conformation is an envelope with O(1′) 0.524 A exo, and the base is oriented syn with respect to the sugar with dihedral angles C(2)-N(1)-C(1′)-O(1′) = 71.2° and C(2)-N(1)-C(1′)-C(2′) = −47.6° which results in the positioning of O(2) almost over the center of the ribose ring. The spin-coupling constants of the proton magnetic resonance spectrum of this cyclic nucleoside derivative measured in C2HCl3 solution confirm the conformation found in the solid state by X-ray methods. There are substantial differences between the experimentally observed coupling constants for the bridged nucleoside and those predicted from the X-ray structure using modified Karplus type relations derived from less strained molecules.

Crystallization of yeast phenylalanine transfer ribonucleic acid

Abstract Two crystalline forms of yeast phenylalanine transfer RNA have been prepared from water-2-methylpentan-2,4-diol and water-tertiary butanol systems. One of the crystal forms has also been produced by the vapour phase method from water-dioxane and both have been produced by precipitation at a waterbutanol-2 interface. One crystal form is orthorhombic (space group C2221, density 1.47), a = 60.5 A , b = 85 A , c = 234 A and has 32 molecules in the unit cell, i.e. four molecules in the asymmetric unit, and the other is a rhombohedral form (space group R32, density 1.51), a rh = 124 A , α rh = 60.8 ° with 36 molecules in the unit cell, i.e. six molecules in the asymmetric unit. Data were collected to a resolution of 15 A with the orthorhombic crystals and to 7 A with the rhombohedral crystals. The orthorhombic form has a large mosaic spread. The crystals are stable. Yeast phenylalanine transfer RNA recovered from the crystals is chargeable to the same extent as the starting material.

X-ray structure of 3′,5′-diacetyl-2′-deoxy-2′-fluorouridine: A pyrimidine nucleoside in the syn conformation

The X-ray structure analysis of 3′,5′-diacetyl-2′-deoxy-2′-fluorouridine is reported. The title compound crystallized from water in the monoclinic space group P21 with cell constants a = 10.874 A, b = 7.379 A, c = 9.971 A, β = 111.41°. The structure was solved by direct methods and refined to a discrepancy index R = 0.039. Contrary to most of the pyrimidine nucleosides the orientation of the nucleobase with respect to the sugar is syn and the conformation about the C(4′)—C(5′) bond is trans—gauche. The ribose exhibits a C(3′)-endo—C(4′)-exo twist conformation and despite the fluoro substitution, bond angles and distances compare well with averaged data for unmodified C(3′)-endo puckered riboses. There are close contacts between the 3′- and 5′-acetate groups which are orientated roughly parallel to each other. The NMR results by Blandin, M., Tran—Dinh, S., Catlin, J.C. and Guschlbauer, W. (1974) Biochim. Biophys. Acta 361, 249–256 (preceding paper), suggest that the conformations in the crystal and in solution are similar.