Unlocking the design principles of programmable RNA catalysts capable of site-specific chemical modification is critical for expanding the functional and therapeutic potential of RNA. The SAM analogue-utilizing ribozyme (SAMURI) enables site-specific RNA alkylation using either S-adenosylmethionine (SAM) or the synthetic cofactor propargylic Se-2,6-diaminopurinribosyl-selenomethionineamide (ProSeDMA), yet the molecular determinants of its reactivity remain incompletely understood. Here, we combined molecular dynamics, 3D-RISM solvation analysis, alchemical free energy calculations, quantum pK_a shift predictions, and ab initio QM/MM free energy simulations to characterize the conformational and electronic factors that govern catalysis. Simulations show that, although the global fold of SAMURI remains stable in solution, the formation of catalytically competent near-attack configurations is rare, indicating that the observed rate depends on access to a minor fraction of these reactive conformations (f_react). A putative Mg²⁺ binding site between the SAM carboxylate and the G30 phosphate, together with a hydrogen bond between the cofactor α-amine and U8:O2, enriches f_react. QM/MM simulations support an S_N2-like alkyl transfer mechanism and show that ProSeDMA reacts more readily than SAM primarily due to its more favorable electronic leaving group properties that enhance the intrinsic rate (k_int). Atomic substitutions at A52 that tune the N3 pK_a enhance nucleophilicity, further lower the activation barrier, and increase k_int. Together, these results show that SAMURI catalysis is governed by a combination of conformational preorganization and electronic effects, providing a framework to guide the design of new programmable RNA alkyltransferases.