The crystal and molecular structure of adenosine triphosphate

Abstract

The three-dimensional structure of the hydrated disodium salt of adenosine triphosphate (Na₂ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 Å. The crystals are orthorhombic, space group P2₁2₁2₁, with a = 30.45(4), b = 20.88(3), c = 7.07(1) Å. There are two molecules of ATP, four sodium ions, and six water molecules in the asymmetric unit. The structure was solved by direct methods and refined to R = 12.3 % using 1118 intensities measured on an automatic diffractometer. The triphosphate chain is in the folded conformation in each of the two crystallographically independent molecules. However, in one molecule (A) it is folded so as to form part of a lefthanded helix, while in the other part of a right-handed helix. There are corresponding differences in the conformations of the ribose rings. The ring is in the envelope conformation with C3' endo in molecule A and C2' endo in molecule B. Two of the sodium ions coordinate the two molecules through the phosphate oxygens and N7 to form an almost centrosymmetric ‘dimer’ which is the fundamental structural unit. The adenine bases show considerable overlap and are stacked in the c axis direction. Details of the hydrogen bonding and the role of water molecules in the structure are discussed.