Biomedical subjects

Dubravka Matković-Calogović

Publications and source records attributed to Dubravka Matković-Calogović.

9 recordsLinked to original sources

PubMed2006

Cyclic trihydroxamic acid derivatives.

In the crystal structures of two cyclic trihydroxamic acid derivatives containing the same substructure unit, viz. 1,3,5-trihydroxy-1,3,5-triazinane-2,4,6-trione dihydrate, C3H3N3O6.2H2O, (I), and 1,3,5-benzyloxy-1,3,5-triazinane-2,4,6-trione, C24H21N3O6, (II), there is no significant difference in the geometric parameters. In (I), there are 11 hydrogen bonds of the O-H...O type interconnecting the molecules in a three-dimensional network, while in (II) there are only two weak C-H...O hydrogen bonds. The results of IR spectroscopic analysis are in good agreement with the crystallographic study.

Acids↗

PubMed2006

Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions.

Tyrosine phenol-lyase, a tetrameric pyridoxal 5'-phosphate dependent enzyme, catalyzes the reversible hydrolytic cleavage of L-tyrosine to phenol and ammonium pyruvate. Here we describe the crystal structure of the Citrobacter freundii holoenzyme at 1.9 A resolution. The structure reveals a network of protein interactions with the cofactor, pyridoxal 5'-phosphate, and details of coordination of the catalytically important K+ ion. We also present the structure of the apoenzyme at 1.85 A resolution. Both structures were determined using crystals grown at pH 8.0, which is close to the pH of the maximal enzymatic activity (8.2). Comparison of the apoenzyme structure with the one previously determined at pH 6.0 reveals significant differences. The data suggest that the decrease of the enzymatic activity at pH 6.0 may be caused by conformational changes in the active site residues Tyr71, Tyr291, and Arg381 and in the monovalent cation binding residue Glu69. Moreover, at pH 8.0 we observe two different active site conformations: open, which was characterized before, and closed, which is observed for the first time in beta-eliminating lyases. In the closed conformation a significant part of the small domain undergoes an extraordinary motion of up to 12 A toward the large domain, closing the active site cleft and bringing the catalytically important Arg381 and Phe448 into the active site. The closed conformation allows rationalization of the results of previous mutational studies and suggests that the observed active site closure is critical for the course of the enzymatic reaction and for the enzyme's specificity toward its physiological substrate. Finally, the closed conformation allows us to model keto(imino)quinonoid, the key transition intermediate.

Apoenzymes↗

PubMed2005

Bis{1-[N-(2-methoxyphenyl)iminomethyl]naphthalen-2(1H)-onato-kappa3O,N,O'}zinc(II) ethanol solvate.

In the crystal structure of the title compound, [Zn(C18H14NO2)2].C2H6O, the Zn atom displays a highly distorted octahedral coordination involving the O and N atoms of two molecules of the Schiff base 1-[N-(2-methoxyphenyl)iminomethyl]naphthalen-2(1H)-one, which acts as an O,N,O'-tridentate ligand. The ethanol molecule is bound to the methoxy group of one ligand molecule via a hydrogen bond.

Journal Article↗

PubMed2004

A new complex of HgBr2 and pyrimidine-2-thione: (pyrimidine-2-thionato-kappaS)(pyrimidinium-2-thionato-kappaS)mercury(II) tetrabromomercury(II).

The title compound, [Hg(C(4)H(4)N(2)S)(C(4)H(3)N(2)S)](2)[HgBr(4)], consists of [Hg(pymt)(pymtH)](+) complex cations (pymtH is pyrimidine-2-thione) lying across twofold rotation axes in space group Fddd, with linearly coordinated mercury at an Hg-S distance of 2.357 (3) A, and [HgBr(4)](2-) anions lying at sites of 222 symmetry. The Hg atom is additionally coordinated by two N and two Br atoms, forming a 2+4 effective coordination sphere. The protonated ligand is connected via N-H.N hydrogen bonds to the neighbouring unprotonated ligand, thus forming infinite chains of cations.

Journal Article↗

PubMed2003

Betainohydroxamic acid chloride.

The title compound, N-hydroxy-2-(trimethylammonio)acetamide chloride, C(5)H(13)N(2)O(2)(+).Cl(-), has been synthesized and structurally characterized. The structure consists of betainohydroxamic acid cations and Cl(-) anions linked by N-H.Cl and O-H.Cl hydrogen bonds into chains along [001]. It was found that the positive inductive effect of the charged N atom in close proximity to the hydroxamate carbonyl O atom has a negligible effect on the hydroxamic C-N bond length.

Journal Article↗

PubMed2003

Polymeric mu-bromo-mu-pyridine-3-carboxylato-kappa3O,O':N-mercury(II).

The asymmetric unit of the title polymeric complex, [HgBr(C(6)H(4)NO(2))](n) or HgBr(nic), contains mercury coordinated via two Br atoms [Hg-Br = 2.6528 (9) and 2.6468 (9) A], two carboxylate O atoms, which form a characteristic four-membered chelate ring [Hg-O = 2.353 (6) and 2.478 (7) A], and an N atom [Hg-N = 2.265 (5) A], in the form of a very irregular (3+2)-coordination polyhedron. The pronounced irregularity of the effective Hg (3+2)-coordination is a result of the rigid stereochemistry of the nicotinate ligand. According to the covalent and van der Waals radii criteria, the strongest bonds are Hg-Br and Hg-N. These covalent interactions form a two-dimensional polymer. The puckered planes are connected by van der Waals interactions, and there are only two intermolecular C-H...O hydrogen bonds [3.428 (10) and 3.170 (10) A].

Journal Article↗

PubMed2003

1,3-Benzothiazole-6-carboxamidinium chloride dihydrate.

The title compound, C(8)H(8)N(3)S(+).Cl(-).2H(2)O, has been synthesized and characterized both spectroscopically and structurally. The structure consists of 1,3-benzothiazole-6-carboxamidinium cations, chloride anions and water molecules, all interconnected by hydrogen bonds into a three-dimensional network. The 1,3-benzothiazole moiety is inclined to the 6-amidine group by 36.71 (9) degrees.

Journal Article↗

PubMed2002

5-Methyl-2-thiouracil.

The molecular structure of the title compound, also known as 2-thiothymine [systematic name: 2,3-dihydro-5-methyl-2-thioxopyrimidin-4(1H)-one], C(5)H(6)N(2)OS, is similar to that of thymine, with only small changes in the ring structure, apart from a significant difference at the substitution site [S=C = 1.674 (1) A]. The molecules are connected by hydrogen bonds, with N-H.O = 2.755 (2) A and N-H.S = 3.352 (1) A. The hydrogen-bond network is different from that in thymine, since it involves all the donor and acceptor atoms.

Journal Article↗

PubMed2001

Aquabromo(6-carboxypyridine-2-carboxylato-O,N,O')mercury(II).

The title compound, [HgBr(C7H4NO4)(H2O)], was obtained by the reaction of an aqueous solution of mercury(II) bromide and pyridine-2,6-dicarboxylic acid (picolinic acid, dipicH(2)). The shortest bond distances to Hg are Hg-Br 2.412 (1) A and Hg-N 2.208 (5) A; the corresponding N-Hg-Br angle of 169.6 (1) degrees corresponds to a slightly distorted linear coordination. There are also four longer Hg-O interactions, three from dipicH(-) [2.425 (4) and 2.599 (4) A within the asymmetric unit, and 2.837 (4) A from a symmetry-related molecule] and one from the bonded water molecule [2.634 (4) A]. The effective coordination of Hg can thus be described as 2+4. The molecules are connected to form double-layer chains parallel to the y axis by strong O-H.O hydrogen bonds between carboxylic acid groups of neighbouring molecules, and by weaker hydrogen bonds involving both H atoms of the water molecule and the O atoms of the carboxylic acid groups.

Crystallography, X-Ray↗