The structure of the cytosine–calcium chloride (1:1) complex. The first evidence for direct binding of calcium to cytosine base

Abstract

The crystal structure of [Ca(C4HsN30)C12] .H20 was determined by X-ray diffraction. The complex crystallizes in the monoclinic space group P2~/c with a = 7.410(1), b = 16.152(2), c = 8.351 (1) A, fl = 107.60 (2) ° and Z = 4. The final R value is 0.070. The Ca 2+ cation is in a pentagonal-bipyramidal environment and is coordinated in the basal plane by two CI atoms, the N(3) and 0(2) atoms of a cytosine base, and 0567-7408/80/081793-05501.00 the 0(2) atom of an adjacent cytosine base. The axial sites are occupied by a C1 atom and an H20 molecule.

Self-assembling of calcium salt of the new DNA base 5-carboxylcytosine

“…The two axial positions are then occupied by one O atom of the carboxylate moiety and one of the three remaining water molecules. Therefore, in (caC)2 -Ca the carboxylic function represents an additional binding site for the metal-ion coordination with respect to the unsubstituted cyto-sine molecule [74]. A similar pentagonal-bipyramidal coordination geometry has been reported in crystals of cytosine-calcium chloride (1:1) complex [74].…”

“…Therefore, in (caC)2 -Ca the carboxylic function represents an additional binding site for the metal-ion coordination with respect to the unsubstituted cyto-sine molecule [74]. A similar pentagonal-bipyramidal coordination geometry has been reported in crystals of cytosine-calcium chloride (1:1) complex [74]. Indeed, in this crystal structure, the Ca 2+ ion is coordinated in the basal plane by two Cl − ions related by the c-glide symmetry, the endocyclic N3 atom and exocyclic O3 atom of a cytosine base, and the O3 atom of an adjacent cytosine base.…”

Synthesis and structure of cytosine dichloride cuprate: direct bonding of copper to cytosine

“…The cytosine ring including the exocyclic 0(2) and amino N(4) atoms is practically planar with a maximum deviation from the least-squares plane of less than 0.03 A except for N(3) and N(4) (0.04 and 0.05 A, respectively). The angle between the two cytosine planes is 7-3 (6) ° , close to the value found in a cytosine calcium polymer (Ogawa et al, 1980). According to previous structural studies, direct binding of a 3d transition metal to base moiety rings is rather unusual, it may be a result of competition between H bonds to form direct Cyt-Cyt pairing or a Cu--Cyt bond.…”

“…X-ray analysis of the structure of a cytosine calcium chloride complex in which the alkali ion is found directly coordinated to the cytosine base (Ogawa, Kumihashi, Tomita & Shirotake, 1980). However, direct cytosine-metal-cytosine binding is rather an exceptional case.…”

Ca2+metal ion adducts with cytosine, cytidine and cytidine 5′-monophosphate: a comprehensive study of calcium reactivity towards building units of nucleic acids

“…In reference to the alkaline-earth metal ions, many X-ray structures of compounds containing Mg 2+ , Ca 2+ and Ba 2+ with nucleic acid constituents have been reported. [27][28][29][30][31][32][33][34] Focusing on Mg(II) and Ba(II), three structures are known: one of Mg 2+ with the nucleobase cytosine 27 and two of Ba 2+ with cytidine-5′-phosphate and uridine-5′-phosphate. 28 The binding mode of the Mg 2+ metal ion with base atoms in cytosine is unidentate via O(2).…”