Table 3.
Relative lifetimes of hydrogen bonds between the incoming nucleobase and amino acid residues of the protein during MD simulations of human TdT complexed either with the primer and dNTP or with an elongated primer.
| TdT–primer–dNTP complex | TdT–elongated primer complex | |||
|---|---|---|---|---|
| H-bond | H-bond lifetime, % | H-bond | H-bond lifetime, % | |
| dGTP | Asp395(COO−)··· (N1H)dGTP | 77.3 | Asp395(COO−)····(N1H)G7 | 76.8 |
| Val394(O backbone) (N2H)dGTP | 49.7 | Val394(O backbone) (N2H)G7 | 37.7 | |
| Asp395(COO−)····(N2H)dGTP | 28.8 | Asp395(COO−)····(N2H)G7 | 28.9 | |
| Glu456(COO−)····(N2H)dGTP | 20.6 | Glu456(COO−)····(N2H)G7 | 26.1 | |
| Arg453(ɛNH) ···(O6)dGTP | 18.2 | Arg453(NH2)····(O6)G7 | 17.2 | |
| Arg453(NH2)····(O6)dGTP | 15.3 | Asp398(COO−)····(N2H)G7 | 12.2 | |
| Val394(O backbone)· (N1H)dGTP | 13.3 | Arg453(ɛNH)···· (O6)G7 | 12.2 | |
| Arg453(ɛNH)····(N7)dGTP | 7.4 | |||
| dATP | Ala396(O backbone) (N6H)dATP | 16.5 | Asp395(COO−)····(N6H)A7 | 9.3 |
| Arg453(NH2)····(N7)dATP | 12.4 | |||
| Arg453(ɛNH)····(N7)dATP | 8.0 | |||
| Val394(O backbone) (N6H)dATP | 5.1 | |||
| dTTP | Asp395(COO−)····(N3H)dTTP | 15.6 | Arg453(NH2)····(O4)T7 | 31.5 |
| Arg457(NH2)····(O4)dTTP | 10.5 | Arg457(NH2)····(O4) T | 15.2 | |
| Arg453(ɛNH)···· (O4)dTTP | 10.0 | Glu456(COO−)····(N3H)T7 | 13.1 | |
| Arg457(ɛNH)····(O4)dTTP | 5.2 | Arg457(ɛNH)····(O4)T7 | 10.6 | |
| Asp398(NH backbone)····(O4)T7 | 8.0 | |||
| Asp398(COO−)····(N3H)T7 | 6.7 | |||
| dCTP | Asp395(COO−)····(N4H)dCTP | 4.2 | Arg457(NH2)····(O2)C7 | 33.8 |
| Arg457(NH2)····(N3)C7 | 22.3 | |||
| Asp395(COO−)····(N4H)C7 | 12.4 | |||