Elementary Patterns in Protein-Nucleic Acid Interactions. IV. Crystal Structure of 3-(Adenin-9-yl)propionamide : 1-Methylthymine (1 : 1) Complex Dihydrate

Abstract

As a ternary interaction model between adenine:thymine base pair and carbamoyl group, 3-(adenin-9-yl)-propionamide: 1-methylthymine complex was prepared and its crystal structure was examined. The crystal exhibits a disordered structure, and the structure unit is a monoclinic cell with dimensions a=11.368(1), b=6.909(1), c=12.708(2) Å, and β=114.49(1)°. The space group is P21 and the unit cell contains two complexes and four water molecules. The base pairing pattern between adenine and thymine is the Hoogsteen type. The carbamoyl group is hydrogen-bonded to N(A1) of adenine in this base pair, the distance NH···N(A1) being 2.94(2) Å. With two kinds of hydrogen bonds of the carbamoyl group, NH···N(A1) above-mentioned and NH···O(carbamoyl), the 3-(adenin-9-yl)propionamide molecules form a sheet extending perpendicular to the c axis; the base-paired thymine molecules extrude alternately from the sheet. Diffused spots along c* with half integers of l can be interpreted as a stacking disorder of the sheets.

Elementary patterns in protein–nucleic acid interactions. VII. Structure of N-[3-(9-adeninyl)propionyl]-DL-tryptophan ethyl ester, C21H23N7O3

“…1. The bond distances and angles are in agreement with those found in 3-(9-adeninyl)propionamide (Takimoto, Takenaka & Sasada, 1981), 3-(9-adeninyl)propionamide: lmethylthymine (l:l) complex dihydrate (Takimoto, Takenaka & Sasada, 1982), 3-(7-adeninyl)-propionamide monohydrate (Takimoto, Takenaka & Sasada, 1983), L-tryptophan hydrochloride (Takigawa, Ashida, Sasada & Kakudo, 1966) and OL-tryptophan ethyl ester hydrochloride (Vijayalakshmi & Srinivasan, 1975). The molecule is extended so that there is no intramolecular stacking between the two rings; the torsion angles being given in Fig.…”

Interligand Interactions Controlling the μ-N7,N9-Metal Bonding of Adenine (AdeH) to the N-Benzyliminodiacetato(2−) Copper(II) Chelate and Promoting the N9 versus N3 Tautomeric Proton Transfer: Molecular and Crystal Structure of [Cu2(NBzIDA)2(H2O)2(μ-N7,N9-Ade(N3)H)]·3H2O

“…A long time ago, studies of base-pair complexes were carried out, and some of them concerned adenine-like:thymine-like examples. [7][8][9][10][11] Very recently we have reported three new modes of adenine-copper(II) coordination and attempted to explain these findings on the basis of interligand interactions in mixed-ligand complexes of N-substituted iminodiacetato-Cu(II) chelates (with Nalkyl, N-benzyl, or N-phenethyl substituents for A, B, and C IDA-like chelating ligands, respectively; phenethyl ) C 6 H 5 CH 2 CH 2 -). 4 On the basis of the above findings we explored a broad series of ternary and quaternary metal + chelating ligand + nucleobase systems, using experimental methods similar to those described elsewhere.…”

Model for interactions of amino acid side chains with Watson-Crick base pair of guanine and cytosine: crystal structure of 9-(2-carbamoylethyl)guanine and 1-methylcytosine complex

“…One approach 0006-2960/85/0424-0508$01.50/0 © 1985 American Chemical Society 9-(2-CARBAMOYLETHYL)GUANINE-l-METHYLCYTOSINE complex to the problem is to use suitable model crystals that contain both the components because protein crystallography has indicated the general trend that the packing density and mean-square displacement of the protein interface with other protein or substrate are similar to those of crystals of small molecules (Richards, 1974;Frauenfelder et al, 1979). Studies of this kind have been done for several combinations and extended to the ternary model systems of adenine-thymine-carbamoyl group (Takimoto et al, 1982) and of adenine-uracil-carboxyl group (Fujita et al, 1983). But Watson-Crick pairing has never been obtained.…”