Structure of the potassium salt of the modified nucleotide dihydrouridine 3'-monophosphate hemihydrate: correlation between the base pucker and sugar pucker and models for metal interactions with ribonucleic acid loops

Abstract

The crystal structure of the potassium salt of dihydrouridine 3'-monophosphate hemihydrate, K+.CgH14 N209P-.½H20, a modified nucleotide, has been determined from three-dimensional X-ray crystallographic data. The nucleotide crystallizes in the space group C2 with unit-cell dimensions a = 22.638 + 0.007, b = 5.765 + 0.001, c = 13.245 + 0.003 A, and fl = 123.31 + 0.01°; Z = 4. Structural solution was obtained by use of the Patterson heavy-atom method followed by successive Fourier syntheses. Positional and thermal parameters were refined by block-diagonal least-squares techniques to a final R of 0.035. The dihydrouracil base is puckered, mainly at C(6), due to saturation of the C(5)-C(6) bond. The furanose ring has a C(2')-endo envelope conformation (2E) with P = 159.0 ° and rm = 39'7 °. A correlation has been found between the nature of the base pucker and the pucker of the sugar: a major pucker at C(6) of the base accommodates a C(2')-endo, O(4')-endo and the C(3')endo sugar puckerings, but a major pucker at C(5) of the base preferentially co-exists with a C(3')-endo pucker. The nucleotide exhibits the anti conformation, with the glycosyl torsion angle Z equal to 71.2 (4) °. The conformation ~, about the exocyclic C(4')-C(5') bond is gauche +. The torsion angle ~p' [C(4')-C(3')0(3')-0] is 215.5 (4) ° and falls within the continuous range of values (190-270 ° ) observed for the known 3'nucleotides. One of the phosphate O atoms is in a nearly eclipsed conformation with respect to the C(3') atom. There is no base-base interaction. Eight ligands, at less than 3.2 A, are coordinated to the K ion: two 0(4) atoms of dihydrouracil bases, an 0(2') atom of the ribose, four phosphate O atoms from two different nucleotide units, and one water O atom. The binding scheme observed here provides insight into possible modes of interaction of K and related metals with RNA's.