The crystal structure of spermidine phosphate trihydrate

Abstract

Spermidine phosphate trihydrate, C7H19N3.~H3PO4.3H20, is found to have a monoclinic unit cell with dimensions, a= 9.22, b= 26.03, c = 6.58/~, fl= 96.0 °. The space group is P21 and the asymmetric unit contains two formula units. The structure was solved by a sharpened Patterson function and refined by the block-matrix least-squares method with anisotropic temperature parameters to an R value of 0.09 for 2868 observed reflexions.The molecules take a normal extended zigzag chain conformation. The chemical formula of this compound has been shown to be [NH+(CH2)3NH+(CH2)4NH+]2.3[HPO4] 2-. 6H20. The structure consists of two kinds of bands, the molecular band and the phosphate--water band. They are extended along the a axis and joined together alternately side by side in the b direction to form a sheet structure with stripes of the bands. Within the molecular band, the spermidine molecules are arranged in parallel along the b axis as is generally seen in aliphatic long chain compounds. The angle of tilt is 90 °. The phosphatewater band consists of dimer and monomer ions of monohydrogen phosphate which are separated by water molecules, forming a network of hydrogen bonds. The striped sheets are piled up alternately along the c axis through N-H. • • O hydrogen bonds in such a way that the phosphate-water band comes next to the molecular band of spermidine. The structure is discussed in comparison with that of spermine phosphate hexahydrate.

Conformational Change of Spermidine upon Interaction with Adenosine Triphosphate in Aqueous Solution

“…The optimized structures of ATP with net charges of À2, À3, and À4 have been deduced by a conformation search and the X-ray data for Na + 2 ATP 2À . [21,22] The conformational changes with a change from pH 3.3 to 5.6 indicate that the increment in gauche conformers is larger for C2ÀC3 (6 %) and C4ÀC5 (6 %) in the butanylene part than for C7 À C8 (3 %) and C8 À C9 (0 %) in the propanylene part (Table 2). At pH 3.3, at which point the average net charge of ATP is À2, the anti orientation of the adenine ring to the ribose is dominant (Figure 4 a).…”

Conformations of Spermine in Adenosine Triphosphate Complex: The Structural Basis for Weak Bimolecular Interactions of Major Cellular Electrolytes

“…The optimized structures of ATP with the net charges of À2, À3, and À4 have been deduced previously (see Figure 4). [16,17] The populations of rotamers about each of the CÀC bonds did not significantly change between pH 5.6 and 7.3 in the presence of ATP (Table 1). At pH 7.3, the g-phosphate becomes divalent, thus leading to tetra-A C H T U N G T R E N N U N G valent ATP.…”

The 1.8‐Å X‐ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding

“…The crystal structure of the free spermidine molecule has already been determined by two groups (Giglio et al, 1966;Huse & Iitaka, 1969). We compared these structures with the 1.8-A structure of spermidine bound to PotD (Fig.…”

“…2). The torsion angles of spermidine trihydrochloride (Giglio et al, 1966), spermidine phosphate trihydrate (Huse & Iitaka, 1969), and spermidine bound to PotD are listed in Table 3. Whereas the backbone conformation of the free spermidine molecule is almost flat, that of the form bound to PotD was bent.…”

“…In the PotD protein, the side Giglio et al (1966). Huse and Iitaka (1969). chain of Gln 327, which is hydrogen bonded to the spermidine amino group, is replaced by Lys 349 in the PotF protein.…”