Table 3.
System Feature | Systems | |||||
---|---|---|---|---|---|---|
A:C | A:G | A(syn):G | T:G | A(syn):A | A:A | |
3.64 | 3.86 | 3.76 | 5.18 (decreases to 4.63 Å over 1– 18 ns) |
3.70 (increases to 5.96 Å over 3–13 ns) |
7.67 (decreases to 3.33 Å over 0– 5 ns and 4.18 Å over 5.5–16 ns) |
|
3.83 | 4.42 | 4.54 (decreases to 3.93 Å over 1.5– 10 ns) |
4.28 | 4.47 (decreases to 4.05 Å over 3 – 13ns)o |
3.50 | |
no | no | no | yes | no | bothb | |
Asp429:Oδ1 | yes | yes | yes | yes | yes | yes |
Asp490:Oδ1 or Oδ2 | yes | yes | yes | both | no | no |
T6:O3′ | yes | yes | yes | no | sometimes | noc |
dNTP:O1α | yes | yes | yes | no | yes | yes |
Number of Water Molecules |
2 | 2 | 2 | 2 | 3 | 2 |
yes | yes | yes | yes | yes | yes | |
Asp427:O | some-times | yes | some-times | no | yes | yes |
Asp429:Oδ2 | yes | yes | yes | yes | yes | yes |
dNTP:O1α | no | no | no | yes | no | no |
dNTP:O1β | yes | yes | yes | yes | yes | yes |
dNTP:O3γ | yes | yes | yes | yes | yes | yes |
Number of Water Molecules |
1 | 1 | 1 | 1 | 1 | 1 |
Average distances over the last nanosecond of the simulation
The second terminal Asp427 oxygen atom replaces the T6:O3′ ligand to the catalytic ion in A:A
The T6:O3′ atom briefly coordinates with the catalytic ion at the beginning of the A:A simulation