Table 3.

Key Active-site Distance and Metal Ion Coordination Data

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

^aAverage distances over the last nanosecond of the simulation

^bThe second terminal Asp427 oxygen atom replaces the T6:O3′ ligand to the catalytic ion in A:A

^cThe T6:O3′ atom briefly coordinates with the catalytic ion at the beginning of the A:A simulation