Complexes between Nucleotide Base and Amino Acid. I. Crystal Structure of Cytosine: N-Formylglycine

Abstract

Cytosine: N-formylglycine complex crystallizes in the space group Pna21 with cell dimensions of a=8.444(2), b=21.169(5), and c=5.120(1) Å. The structure was solved by the trial-and-error method on the basis of a Patterson map. A full-matrix least-squares refinement led to an R value of 0.035. The difference map revealed the protonation of cytosine by the carboxyl group of N-acylamino acid and the involvement of ionic interaction in complex formation. This mode is the same as proposed for cytosine: N-benzoylglycine complex in spite of different molecular environment. Such arrangement of cytosine and ionized carboxyl group of amino acid may suggest a mutual recognition scheme between nucleic acid and protein.

Bis(2-aminopyridinium) sulfate

“…The crystal packing is stabilized by a series of N-HÁ Á ÁO hydrogen bonds (Table 2 and Fig. 2) in a hydrogen-bonding pattern similar to those found in 2-aminopyridinium carboxylate complexes (Bis et al, 2005) and cytosine carboxylates (Ohki et al, 1975;Tamura et al, 1972). View of (I), shown with 50% probability displacement ellipsoids.…”

Hydrogen-bonding patterns of 2-aminopyridiniump-nitrobenzoate

“…Protonated 2-aminopyridine forms a fork-like hydrogen bonding pattern with the carboxylate group. This fork-like interaction is observed in cytosine carboxylate interactions (Ohki et al, 1975;Tamura et al, 1972). The nature of the interaction and the mode of hydrogen bonding are quite similar to those found in 2-aminopyridinium carboxylate complexes (Joanna & Zaworotko, 2005).…”

Cytosinium 3,5-dinitrosalicylate

“…The crystal structures of a number of inorganic cytosinium salts are known [chloride (Mandel, 1977), nitrate (Cherouana et al, 2003), dihydrogenphosphate (Jaskó lski, 1989;Bagieu-Beucher, 1990), pentaiodide (Wang et al, 2001) and the cyclophosphate (Swamy et al, 2001)]. Cytosinium salts of organic acids are also common, the structures of a number of these, including some with N-protected amino acids, having been reported [Nformylglycinate (Ohki et al, 1975), N-benzoylglycinate (Tamura et al, 1972; Gö rbitz & Sagstuen, 2004) (105 K), N,N-phthaloylglutamate (Takenaka et al, 1980), trichloroacetate (Gdaniec et al, 1989), resorcylate (Tamura et al, 1973) and hydrogen maleate (Balasubramanian et al, 1996)]. An unusual proton-transfer compound with the dye orange G [disodium 7hydroxy-8-(phenylazo)-1,3-naphthalenedisulfonate] is also known (Ojala et al, 1994)], as well as the nucleoside 1-(-darabinofuranosyl)cytosine (Sherfinski & Marsh, 1973).…”