Table 2. EVB/FEP States for Modeling of the GB and SB Pathways of the Nucleotidyl-Transfer Reaction in the Water, Polβ, and Polλ Systemsa.
| state | GB | SB |
|---|---|---|
| RS | Oδ(−0.8514) + H3t–Onuc + Pα–Olg | H3t–Onuc + Pα–Olg |
| IS1 | Oδ–H3t + Onuc(−0.8549) + Pα–Olg | Onuc(−0.8549) + Pα–Olg |
| IS2a | Oδ–H3t + Onuc···(1.90 Å)···Pα···(1.90 Å)···Olg | Onuc···(1.90 Å)···Pα···(1.90 Å)···Olg |
| IS2b | Oδ–H3t + Onuc···(2.28 Å)···Pα···(2.25 Å)···Olg | Onuc···(2.28 Å)···Pα···(2.25 Å)···Olg |
| PS | Oδ–H3t + Onuc–Pα + Olg(−0.8100) | Onuc–Pα + Olg(−0.8100) |
a
Each state is described schematically by the atoms or atomic groups most directly involved in the formation and cleavage (···) of the covalent bonds (−). Atomic charges of selected atoms are indicated in superscripts, and distances between the oxygen and phosphorus atoms in IS2 and IS2b are given in parentheses. See Tables S6–S28 for the full description of the EVB/FEP states. The missing proton in the IS1, IS2, and PS states in the SB pathway was compensated by sodium and/or chloride ions in the water systems, and by a charged arginine or a sodium ion in the Polβ and Polλ systems (see Tables S1 and S3).