The crystal and molecular structure of adenosine triphosphate

Abstract

The three-dimensional structure of the hydrated disodium salt of adenosine triphosphate (Na 2 ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 Å. The crystals are orthorhombic, space group P 2 1 2 1 2 1 , 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.

The 1.3 Å resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction

“…Interestingly, the monovalent ions described in these studies as well as the sodium ions reported in the MeRNA database (Stefan et al 2006) display larger distances between the Na + ions and their ligands (between 2.8 and 3.2 Å ). These distances are significantly larger than the ones observed in our structure and in other high-resolution structures of nucleotides (Kennard et al 1971). It is therefore possible that the longer distances that are observed at a lower resolution reflect the presence of hybrid binding sites with partial occupancies that combine water and sodium ions (McFail-Isom et al 1999).…”

“…Since the occupancies of both sodium cations are close to unity, it is likely that they simultaneously occupy this binding site. The geometry of the disodium coordination is close to that observed in the structure of ATP (Kennard et al 1971). However, the binding environment is different.…”

Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H2O

“…12H20 (Kennard et al, 1971). Further, the geometries of the pyrophosphate groups of these ADP molecules will be described together with those in CDP, CDP-choline (Viswamitra, Seshadri, Post & Kennard, 1975) and K2UDP.…”

The crystal and molecular structure of 3-methoxypentafluorotropone at − 50°C

“…The structure was solved by direct methods (Germain & Woolfson, 1968) and tangent refinement of phases with the automatic phasing program TANFIZ (Kennard, Isaacs, Motherwell, Coppola, Wampler, Larson & Watson, 1971). Phases (0 ° or 180 °) were assigned to 147 of the 151 reflexions with E> 1.40, and from the E map calculated with these phases, the seven-membered ring and the seven atoms bonded directly to the ring atoms were located.…”