Table 2. Distance from ions to specific nucleic acid atoms for direct binding.
| Na+(K+) distances (Å) | ||||||
|---|---|---|---|---|---|---|
| B-DNA | O6(G6) | O6(G18) | N4(C7) | N4(C19) | ||
| 2.38 ± 0.13(2.78 ± 0.17) | 2.40 ± 0.14(2.80 ± 0.19) | 3.72 ± 0.50(3.87 ± 0.56) | 3.58 ± 0.54(4.06 ± 0.61) | |||
| Z-DNA | OP1(G8) | OP1(G20) | OP2(G8) | OP2(G20) | O3′(C7) | O3′(C19) |
| 2.39 ± 0.15(2.82 ± 0.20) | 2.36 ± 0.13(2.80 ± 0.19) | 3.86 ± 0.36(4.11 ± 0.39) | 4.12 ± 0.30(4.13 ± 0.41) | 3.96 ± 0.26(3.39 ± 0.54) | 3.97 ± 0.27(3.37 ± 0.52) | |
| A-RNA | O6(G6) | O6(G18) | N4(C7) | N4(C19) | ||
| 2.36 ± 0.11(2.79 ± 0.17) | 2.39 ± 0.14(2.78 ± 0.18) | 3.13 ± 0.52(3.54 ± 0.36) | 3.59 ± 0.38(3.66 ± 0.40) | |||
| Z-RNA | O2(C7) | O2(C19) | O2′(C7) | O2′(C19) | ||
| 2.39 ± 0.13(2.83 ± 0.21) | 2.39 ± 0.12(2.79 ± 0.18) | 2.43 ± 0.13(2.80 ± 0.15) | 2.44 ± 0.13(2.77 ± 0.14) | |||
The labels in the parenthesis refer to the residues to which the atoms belong. Usually four to six atoms act to form a single ion trap in the middle part of a duplex, as shown in Figure 14. The distances are averages and are based on the last 10 ns of MD simulations.