Table 2.

Comparision of the equivalent cations bound in viral RNA polymerases to the structural manganese in ϕ6 RdRP

Virus	PDB ID	RMSD distance (Å)a	Percentage of ϕ6b	Published ion	Resolution (Å)	Distance from ϕ6 Mn2+c	Comments
WNV	2hcn	2.7	40	Ca2+	2.4	1.6	From map and coordination geometry it is unlikely to be Ca2+
WNV	2hfz	2.9	50	Mg2+	2.8	1.3	Map and coordination geometry consistent with Mg2+
FMDV	1wne	2.8	51	Mg2+	3.0	1.6	Structure factors not available
RHDV	1khv	2.8	52	(H2O)	2.5	–	Lu3+ ion 6.0 Å from Mn2+ in ϕ6. Evidence for Mg2+ in place of H2O at Mn2+ site
RHDV	1khw	2.7	52	–	2.7	–	Poor density in region of active site makes interpretation difficult
NV	1sh3	2.8	52	Mg2+	3.0	0.9	Map and coordination geometry consistent with Mg2+
NV	3bso	2.8	52	(H2O)	1.7	1.4	Water molecule present in equivalent position in the elongation complex
DV	2j7u	2.8	50	Mg2+	1.9	1.8	Map and coordination geometry consistent with Mg2+
PV	1rdr	2.9	33	Ca2+	2.4	2.1	From map and coordination geometry it is unlikely to be Ca2+
RV	1mwh	2.9	42	Mn2+	2.5	1.0	Cap bound structure with Mn2+ion bound in equivalent site
RV	1n35	2.8	42	–	2.5	–	No ion present in equivalent position

^aRMSD of structurally matched Cα atom positions.

^bPercentage of ϕ6 RdRp structurally equivalenced.

^cDistance of the metal ion binding site from the Mn²⁺-binding site of ϕ6 RdRp. Based on superposition of Cα atoms using SHP (62) (see Materials and methods section).