	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 3r8s:A3026, See in JSmol MgRNA representative site for type cis-2OP

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Site type: cis-2O_ph

Schematic drawing for
cis-2O_ph
MgRNA type cis-2OP

List of all 6585 Mg²⁺ binding sites with the site type cis-2O_ph in RNA crystal structures in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv ^#", "Qs ^#", "Qe ^#", "PDB ID" or "Mg²⁺ ID"
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Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
1cx0	B407	cis-2O_ph	2	0.05	0.54	0.95	no
1drz	B403	cis-2O_ph	2	0.05	0.54	0.80	no
1ehz	A540	cis-2O_ph	5	0.92	0.80	0.99	yes
1evv	A902	cis-2O_ph	4	0.84	0.69	0.73	yes
1ffy	T1209	cis-2O_ph	6	0.58	0.93	0.96	yes
1fjg	A1547	cis-2O_ph	2	0.21	0.20	0.64	no
1fjg	A1599	cis-2O_ph	2	0.21	0.32	0.60	no
1fjg	A1617	cis-2O_ph	2	0.13	0.10	0.61	no
1fjg	A1578	cis-2O_ph	2	0.27	0.15	0.37	no
1fjg	A1553	cis-2O_ph	2	0.16	0.47	0.57	no
1fjg	A1606	cis-2O_ph	2	0.13	0.19	0.66	no
1fjg	A1575	cis-2O_ph	2	0.22	0.20	0.64	no
1hc8	C1165	cis-2O_ph	2	0.21	0.22	0.92	no
1hc8	D1363	cis-2O_ph	2	0.14	0.17	0.92	no
1hc8	C1163	cis-2O_ph	2	0.20	0.21	0.85	no
1hnw	A1597	cis-2O_ph	2	0.40	0.44	0.48	no
1hnw	A1604	cis-2O_ph	2	0.12	0.27	0.47	no
1hnw	A214	cis-2O_ph	2	0.06	0.24	0.57	no
1hnw	A1552	cis-2O_ph	2	0.41	0.39	0.56	no
1hnw	A1615	cis-2O_ph	2	0.14	0.17	0.61	no
1hnw	A1546	cis-2O_ph	2	0.29	0.31	0.52	no
1hnw	A1574	cis-2O_ph	2	0.18	0.24	0.51	no
1hnw	A1577	cis-2O_ph	2	0.17	0.16	0.46	no
1hnx	A1552	cis-2O_ph	2	0.38	0.24	0.48	no
1hnx	A1546	cis-2O_ph	2	0.18	0.23	0.55	no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Abbreviations used for Mg²⁺ "Site type"	Mg²⁺ inner-sphere ligands	Geometry for inner-sphere O_P	Mg²⁺ outer-sphere moieties
Site type used in the classification is a string abbreviation of ligand composition in Mg²⁺ coordination sphere
Abbreviations used for Mg²⁺ "Site type"	O_ph phosphate oxygen (OP1/OP2) O_r ribose oxygen (O2'/O4') or oxygen bridging phosphate and ribose (O3'/O5') O_b nucleobase oxygen N_b nucleobase nitrogen	*cis-* two O_P ligands adopt cis- isoform *trans-* two O_P ligands adopt trans- isoform *fac-* three O_P ligands adopt fac- isoform *mer-* three O_P ligands adopt mer- isoform	P_out phosphate moiety R_out ribose moiety B_out nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Site type: cis-2Oph

MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures

Site type: cis-2O_ph