	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 2wdg:Z735, See in JSmol MgRNA representative site for type 2OR

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Site type: 2O_r

Schematic drawing for
2O_r
MgRNA type 2OR

List of all 560 Mg²⁺ binding sites with the site type 2O_r 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
1hnw	A1617	2O_r	2	0.09	0.11	0.56	no
1hnx	A1618	2O_r	2	0.04	0.11	0.52	no
1hnz	A1618	2O_r	2	0.10	0.13	0.45	no
1hnz	A1569	2O_r	2	0.10	0.35	0.17	no
1hnz	A1613	2O_r	2	0.04	0.61	0.52	no
1hr0	A1593	2O_r	3	0.54	0.23	0.67	no
1i94	A1528	2O_r	3	0.26	0.44	0.84	no
1i95	A1523	2O_r	2	0.04	0.10	0.54	no
1i95	A1529	2O_r	2	0.13	0.12	0.83	no
1i96	A1523	2O_r	2	0.06	0.10	0.59	no
1i96	A1529	2O_r	2	0.17	0.23	0.85	no
1i97	A1524	2O_r	2	0.15	0.18	0.73	no
1i97	A1529	2O_r	3	0.13	0.40	0.96	no
1ibm	A1648	2O_r	2	0.12	0.13	0.63	no
1ibm	A1600	2O_r	4	0	0.68	0.29	no
1jj2	08075	2O_r	6	0.43	0.81	0.85	no
1k73	A8075	2O_r	6	0.49	0.60	0.60	no
1k8a	A8075	2O_r	6	0.47	0.57	0.87	no
1k9m	A8075	2O_r	6	0.67	0.45	0.85	no
1kc8	A8075	2O_r	6	0.79	0.52	0.67	no
1kd1	A8075	2O_r	6	0.65	0.55	0.78	no
1kd1	A8119	2O_r	2	0.10	0.39	0.67	no
1kqs	08075	2O_r	6	0.61	0.59	0.79	no
1m1k	A8075	2O_r	6	0.34	0.81	0.82	no
1m90	A8075	2O_r	6	0.45	0.75	0.73	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: 2Or

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

Site type: 2O_r