	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 2qex:08096, See in JSmol MgRNA representative site for type 2OB-NB

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Site type: 2O_b·N_b

Schematic drawing for
2O_b·N_b
MgRNA type 2OB-NB

List of all 127 Mg²⁺ binding sites with the site type 2O_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
1hnw	A1549	2O_b·N_b	3	0.08	0.28	0.68	no
1vvl	A1662	2O_b·N_b	3	0.41	0.22	0.81	no
1vvl	A1609	2O_b·N_b	3	0.37	0.14	0.77	no
1vvm	A3227	2O_b·N_b	3	0.31	0.13	0.75	no
1vvm	A3116	2O_b·N_b	3	0.47	0.30	0.87	no
1vvp	A1608	2O_b·N_b	3	0.40	0.18	0.92	no
1vvp	A1661	2O_b·N_b	3	0.42	0.21	0.59	no
1vvq	A3229	2O_b·N_b	3	0.35	0.23	0.85	no
1vvs	A3070	2O_b·N_b	3	0.40	0.27	0.67	no
1vvu	A3116	2O_b·N_b	3	0.52	0.39	0.06	no
1vvw	A3144	2O_b·N_b	3	0.17	0.41	0.64	no
1vx8	A1661	2O_b·N_b	3	0.43	0.31	0.46	no
1vx8	A1608	2O_b·N_b	3	0.34	0.18	0.46	no
1vxj	A3228	2O_b·N_b	3	0.06	0.27	0.91	no
1vxj	A3135	2O_b·N_b	3	0.35	0.23	0.12	no
1vxj	A3174	2O_b·N_b	3	0.06	0.33	0.56	no
1vxk	A1608	2O_b·N_b	3	0.39	0.12	0.91	no
1vxl	A3220	2O_b·N_b	3	0.08	0.28	0.74	no
1vxn	A3137	2O_b·N_b	3	0.42	0.22	0.33	no
1vxn	A3229	2O_b·N_b	3	0.08	0.18	0.47	no
1vxq	A3226	2O_b·N_b	3	0.37	0.22	0.88	no
1vxt	A3135	2O_b·N_b	3	0.37	0.15	0.56	no
2j00	Z234	2O_b·N_b	3	0.18	0.22	0.62	no
2nok	B130	2O_b·N_b	3	0.29	0.07	0.60	no
2qex	08096	2O_b·N_b	6	0.65	0.65	0.71	yes

^# 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·Nb

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

Site type: 2O_b·N_b