	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 2r8s:R1004, See in JSmol MgRNA representative site for type 2OB

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Site type: 2O_b

Schematic drawing for
2O_b
MgRNA type 2OB

List of all 1662 Mg²⁺ binding sites with the site type 2O_b 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
1jj2	08042	2O_b	6	0.34	0.96	0.95	no
1m1k	A8042	2O_b	6	0.33	0.79	0.94	no
3cc7	08076	2O_b	6	0.33	0.87	0.85	no
1q81	A8042	2O_b	6	0.33	0.44	0.49	no
3ccu	08075	2O_b	6	0.33	0.90	0.80	no
1q81	A8097	2O_b	6	0.33	0.72	0.65	no
4dv5	A1626	2O_b	4	0.33	0.35	0.76	no
1vqo	08042	2O_b	6	0.32	0.88	0.72	no
3ccu	08076	2O_b	6	0.32	0.90	0.70	no
1yi2	08097	2O_b	6	0.32	0.86	0.94	no
1n8r	A8042	2O_b	6	0.32	0.74	0.61	no
1yhq	08032	2O_b	6	0.32	0.82	0.81	no
4kvb	A1736	2O_b	2	0.32	0.56	0.90	no
1yj9	08097	2O_b	6	0.32	0.75	0.74	no
1yij	08097	2O_b	6	0.32	0.89	0.85	no
4dha	A3678	2O_b	4	0.32	0.58	0.93	no
1vq5	08097	2O_b	6	0.32	0.84	0.94	no
3ccq	08076	2O_b	6	0.32	0.89	0.92	no
1vvy	A3117	2O_b	2	0.32	0.43	0.81	no
1qvf	08042	2O_b	6	0.31	0.80	0.90	no
3v27	A3413	2O_b	4	0.31	0.42	0.96	no
1vq4	08097	2O_b	6	0.31	0.85	0.92	no
3v23	A3360	2O_b	5	0.31	0.50	0.71	no
1vqo	08097	2O_b	5	0.31	0.67	0.79	no
1kc8	A8042	2O_b	6	0.31	0.79	0.90	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: 2Ob

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

Site type: 2O_b