	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 1vqo:08005, See in JSmol MgRNA representative site for type mer-3OP

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Site type: mer-3O_ph

Schematic drawing for
mer-3O_ph
MgRNA type mer-3OP

List of all 1181 Mg²⁺ binding sites with the site type mer-3O_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
1fjg	A1600	mer-3O_ph	3	0.35	0.62	0.60	no
1fjg	A1585	mer-3O_ph	3	0.38	0.35	0.66	no
1gid	B270	mer-3O_ph	3	0.42	0.61	0.78	no
1gid	A268	mer-3O_ph	3	0.39	0.65	0.76	no
1hnw	A1593	mer-3O_ph	3	0.39	0.51	0.48	no
1hnw	A1583	mer-3O_ph	3	0.44	0.36	0.50	no
1hnw	A1598	mer-3O_ph	3	0.49	0.33	0.50	no
1hnx	A1594	mer-3O_ph	3	0.35	0.47	0.50	no
1hnx	A1599	mer-3O_ph	3	0.40	0.48	0.55	no
1hnx	A1584	mer-3O_ph	3	0.34	0.35	0.52	no
1hnz	A1599	mer-3O_ph	3	0.39	0.59	0.52	no
1hnz	A1584	mer-3O_ph	3	0.43	0.35	0.52	no
1hr0	A1598	mer-3O_ph	3	0.35	0.68	0.67	no
1hr0	A1583	mer-3O_ph	3	0.35	0.37	0.68	no
1hr2	B4	mer-3O_ph	6	0.98	0.93	0.99	yes
1hr2	A3	mer-3O_ph	6	0.96	0.86	0.93	yes
1i94	A1540	mer-3O_ph	3	0.17	0.60	0.92	no
1i95	A1542	mer-3O_ph	3	0.10	0.54	0.93	no
1i96	A1542	mer-3O_ph	3	0.18	0.35	0.97	no
1i97	A1542	mer-3O_ph	3	0.23	0.50	0.74	no
1ibk	A1588	mer-3O_ph	3	0.24	0.45	0.43	no
1ibk	A1593	mer-3O_ph	3	0.43	0.69	0.45	no
1ibk	A1578	mer-3O_ph	3	0.28	0.49	0.46	no
1ibl	A1577	mer-3O_ph	3	0.37	0.44	0.46	no
1ibm	A1593	mer-3O_ph	3	0.39	0.32	0.38	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: mer-3Oph

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

Site type: mer-3O_ph