Deoxyadenosine crystal structure

So far only a few dozen organofluorine compounds have been isolated from living organisms, for example fluoroacetic acid, 4-fluorothreonine and rw-fluoro-oleic acid [244-246], The reason that nature has not invested in fluorine chemistry could be a combination of low availability of water-dissolved fluoride in the environment due to its tendency to form insoluble fluoride salts, and the low reactivity of water-solvated fluoride ion. However, in 2002, O Hagan and collaborators [247] published the discovery of a biochemical fluorination reaction in a bacterial protein extract from Streptomyces cattleya converting S-adenosyl-L-methionine (SAM) to 5 -fluoro-5 deoxyadenosine (5 -FDA). The same protein extract contained also the necessary enzymatic activity to convert 5 -FDA into fluoroacetic acid. In 2004, the same authors published the crystal structure of the enzyme and demonstrated a nucleophilic mechanism of fluorination [248,249]. 

The discussion in Section 18.4.1.4 on adenine mentions that the radiation chemistry of the two nucleosides adenosine and deoxyadenosine are very different. In adenosine one observes the A(N6-H) radical, while in deoxyadenosine the site of oxidation is on the deoxyribose. These two structures differ only at the C2 position. A small environmental change in the crystal structure seems to have a large effect on the trapping site of the oxidative product. It would be very interesting to know just what small changes in the environment are important here. 

Crystal structures of several 9-substituted adenines including 9-methyladenine (63AX907, 77AX(B)253), adenosine (72AX(B)1982), and 2 -deoxyadenosine (65AXiii) confirm the 6-amino structure. Additional references are given in a review (76AHC(Sl)502). 

Figure 23 A crystal structure of MCM from Propionibacterium shermanii. Shown on the left Is a ribbon diagram of the two subunits of MCM, with cob(ll)alamin, 5 -deoxyadenosine, and succinyl-or malonyl-CoA bound to MutA(gray). MutB is shown in green. The illustration was generated from PDF 4req. °...

Then the 7,8-diaminononanoate (7,8-diaminopelargonic acid) (Scheme 12.93) is converted to the bisamide dethiobiotin (an imidazolidone) by carboxylation with carbon dioxide (CO2) in the presence of ATP in a reaction requiring magnesium (Mg+ ) and catalyzed by dethiobiotin synthase (EC 6.3.3.3). The well-known reversible reaction of amines with carbon dioxide (CO2) and an X-ray crystal structure showing the 8-amino group as a mixed carbonic phosphate anhydride has lent support to this picture (PDB la82). Finally, in the presence of biotin synthase (EC 2.8.1.6), an enzyme that appears to be used only once in each synthesis, reaction occurs with 2 equivalents (but almost certainly one at a time) of SAM and sulfur to produce biotin, 2 equivalents of methionine (Met, M), and 2 equivalents of 5 -deoxyadenosine. 

Cyclic Cs-trinuclear complexes [(Cp RhLls] " [L = adenosine (Hado) 158, 2 -deoxyadenosine (Hdeoado) 159, and 5 -acetyl-2, 3 -isopropylideneadenosine (Haipado) 160] were prepared and characterized by UVA is and circular dichroism spectra, NMR spectroscopy, electrospray ionization mass spectroscopy, and X-ray crystal structure analysis. ... 

It can be seen that alkylation has changed the sugar-base conformation (distant from the site of alkylation) from anti (as in deoxyadenosine and in B-DNA) to syn (as in alkylated deoxyadenosine and in some bases in Z-DNA). The sugar puckers are either C2 -endo or C3 -endo. A second structural feature of great interest in these crystals is that the more planar anthracene portion of the PAH is stacked between adenine residues of other molecules throughout the crystal. The highly buckled region of the PAH does not take part... 

The adenine radical cation was observed in a single crystal of adenine hydrochloride hemihydrate [43]. In this crystal, the adenine is protonated at Nl. After electron loss, the molecule deprotonates at Nl, giving Ade(Nl -l-H, Nl-H). This produces a radical that is structurally equivalent to the cation of the neutral adenine molecule with spin density on C8 and N6 [p(C8) = 0.17 and p(N6) = 0.25]. The adenine radical cation is strongly acidic (pi a< 1) [22]. This strong driving force makes the reaction independent of environmental conditions. In single crystals of adenosine [42] and anhydrous deoxyadenosine [44], the N6 deprotonated cation [Ade(N6-H) ] is observed which is characterized by p(C8) = 0.16 and p(N6) = 0.42. The experimental isotropic hyperfine couplings are N6-H = 33.9 MHz and C8-H = 12.4 MHz. 

Fig. 7. Stereodrawing of the molecular structure of JV-benzoyl-5 0-/ert-butyldimethylsi-lyl-2 -deoxyadenosine monohydrate drawn with ORTEPU. (Johnson, 1967). There is an intramolecular C—H O hydrogen bond between C-8 and 0-5, which is indicated by a solid line drawn between them [C-8—H 0-5 = 3.241(11) A]. In addition, there is a C—H O hydrogen bond between C-6 of the benzyl ring and the water of crystallization [C-6(benzyl)—H O(water) = 3.197(11) A].

Rohrer DC, Sundaralingam M (1970) Stereochemistry of nucleic acids and their constituents. XII. Crystal and molecular structure of a-D-amino-2 -deoxyadenosine monohydrate. J Am Chem Soc 92 4956 962... 

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