	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 1hr2:A5, See in JSmol MgRNA representative site for type OB-NB

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Site type: O_b·N_b

Schematic drawing for
O_b·N_b
MgRNA type OB-NB

List of all 592 Mg²⁺ binding sites with the site type O_b·N_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
1qvf	08102	O_b·N_b	6	0.30	0.83	0.97	no
1qvg	08102	O_b·N_b	6	0.51	0.86	0.69	yes
1s72	08102	O_b·N_b	6	0.27	0.88	0.66	no
1vq4	08102	O_b·N_b	6	0.31	0.97	0.80	no
1vq5	08102	O_b·N_b	5	0.35	0.76	0.92	no
1vq6	08102	O_b·N_b	6	0.35	0.88	0.86	no
1vq7	08102	O_b·N_b	6	0.24	0.87	0.89	no
1vq8	08102	O_b·N_b	6	0.30	0.93	0.70	no
1vq9	08102	O_b·N_b	5	0.26	0.79	0.60	no
1vq9	08084	O_b·N_b	5	0.56	0.67	0.30	no
1vqk	08102	O_b·N_b	6	0.33	0.81	0.75	no
1vql	08102	O_b·N_b	6	0.26	0.90	0.75	no
1vqm	08102	O_b·N_b	6	0.21	0.76	0.77	no
1vqn	08102	O_b·N_b	6	0.20	0.62	0.88	no
1vqo	08102	O_b·N_b	6	0.32	0.89	0.93	no
1vqp	08102	O_b·N_b	6	0.30	0.91	0.81	no
1vvl	A1637	O_b·N_b	2	0.38	0.07	0.99	no
1vvm	A3138	O_b·N_b	2	0.36	0.07	0.85	no
1vvm	A3102	O_b·N_b	2	0.35	0.13	0.51	no
1vvm	A3192	O_b·N_b	2	0.41	0.21	0.80	no
1vvm	A3122	O_b·N_b	2	0.49	0.21	0.87	no
1vvm	A3193	O_b·N_b	2	0.35	0.10	0.83	no
1vvo	A3130	O_b·N_b	2	0.38	0.12	0.68	no
1vvp	A1636	O_b·N_b	2	0.40	0.04	0.22	no
1vvq	A3195	O_b·N_b	2	0.37	0.14	0.26	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: Ob·Nb

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

Site type: O_b·N_b