Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes

ABSTRACT

The X-ray diffraction (XRD) structures for new isoforms of [M(H₂O)₆]·[M(HATP)₂]·2(HDPA)·xH₂O, ATP = adenosine 5’-triphosphate, DPA = 2,2’-dipyridylamine, M = Mg(II), x = 6H₂O, 1, M = Ca(II), x = 8H₂O, 2 were determined by using rotating anode on molybdenum target X-ray source and Kappa CCD with confocal focusing mirror. The accuracy of the presently refined structure for 1 is the highest reported so far based on agreement factors (R1 = 0.0579) and estimated standard deviations (esds) on geometrical parameters. The comparative analysis was extended to the structures of other low molecular weight metal-triphosphate complexes, to the structures of metal-triphosphate-protein systems as well as to computed models of metal-triphosphate complexes. The structures of 1 and 2 reported in this work show that on changing the number of co-crystallized water molecules, the interaction of the metal to the phosphate chain (for 1) and the conformation of ribose (for 2) undergo subtle but significant changes. Interestingly, the vast majority of Mg-nucleoside triphosphate (NTP)-enzyme systems have similar pattern of coordination to the phosphate chain when compared to 1 and 2. The three phosphate groups have variable M-O bond distances, depending on the systems. The structures for 1 and 2 have a high significance as general model compounds for experimental solid state and computations for these types of biological systems.

Keywords:

Single-crystal X-ray diffraction, Adenosine triphosphate, ATP, Adenosine diphosphate, Magnesium, Calcium, Metal ion.