   2.4.2.5 | more |
enzyme homology structure modeling and molecular dynamics simulations, overview. Nucleophilic attack on C1' by the carboxylate of the catalytic residue Glu85. Pro11 and Pro42 play a prominent role in making up the active site cavity where one of the Asp79 carboxylate oxygens and the carboxamide nitrogen of Asn113 recognize the O5' of the sugar moiety of the substrate while the backbone NH of Ala10 hydrogen bonds to O3'. The heteroaromatic ring of the nucleobase thus gets sandwiched between the phenyl rings of Phe12 and Phe13, on one side and the hydrophobic sidechains of Phe56 and Leu119 on the opposite side. The Met120 side chain sulfur appears close to the H1' atom, which suggests that it likely plays a role, together with the carboxylate of Asp62, in stabilization of the oxocarbenium reaction intermediate |
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