. Author manuscript; available in PMC: 2011 Apr 5.

Published in final edited form as: Biochemistry. 2011 Mar 9;50(13):2672–2682. doi: 10.1021/bi2000164

Table 1.

Metal ion residency at the reverse G•U wobble site for product and precleaved forms.

Structure	Trajectory	Mg²⁺ present initially	Mg²⁺ residency (%)	Na⁺ residency (%)
Product (C75°)
	1	No	0	94
	2	No	0	99
	1	Yes	86	12
	2	Yes	100	0
Precleaved (C75⁺)
	1	Yes	100	0
	2	Yes	100	0
	1	No	0	93
	2	No	0	99

Percentage residency of metal ions at the reverse G•U wobble site for product C75° and precleaved C75⁺ states from MD simulations is presented. Metal ion residency is defined as the percentage of time during the trajectory in which a Mg²⁺ or Na⁺ ion, as appropriate, is located within 5 Å from at least one of the following three atoms: G25(N7), G25(O6), or U20(O2). This distance is consistent with observed second shell ligands (91). Results are obtained from 25 ns trajectories, with data points taken every 5 ps.