	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
1vxn	A3229	2O_b·N_b	3	0.08	0.18	0.47	no
1vvq	A3229	2O_b·N_b	3	0.35	0.23	0.85	no
3ohj	A3121	2O_b·N_b	3	0.09	0.54	0.37	no
3i8h	A1741	2O_b·N_b	3	0.05	0.23	0.50	no
3kiy	A3171	2O_b·N_b	3	0.08	0.24	0.94	no
3u5h	53839	2O_b·N_b	3	0.06	0.52	0.97	no
3knh	A1627	2O_b·N_b	3	0.06	0.26	0.82	no
4aqy	A2545	2O_b·N_b	3	0.10	0.21	0.75	no
4nvx	A3003	2O_b·N_b	3	0.10	0.40	0.50	no
4nw1	A3003	2O_b·N_b	3	0.07	0.50	0.60	no
1hnw	A1549	2O_b·N_b	3	0.08	0.28	0.68	no
1vvp	A1608	2O_b·N_b	3	0.40	0.18	0.92	no
2nok	B130	2O_b·N_b	3	0.29	0.07	0.60	no
4qcz	A3016	2O_b·N_b	3	0.13	0.33	0.95	no
4qd1	A3018	2O_b·N_b	3	0.05	0.33	0.80	no
4ji1	A1635	2O_b·N_b	3	0.04	0.35	0.97	no
3knj	A1571	2O_b·N_b	3	0.09	0.19	0.56	no
4ji5	A1639	2O_b·N_b	3	0.06	0.30	0.69	no
4b3m	A2580	2O_b·N_b	3	0.16	0.47	0.98	no
4duz	A1646	2O_b·N_b	3	0.07	0.33	0.93	no
4qcn	A3050	2O_b·N_b	3	0.08	0.36	0.80	no
4tpc	A1657	2O_b·N_b	3	0.85	0.41	0.95	no
1vvp	A1661	2O_b·N_b	3	0.42	0.21	0.59	no
1vx8	A1661	2O_b·N_b	3	0.43	0.31	0.46	no
1vvl	A1662	2O_b·N_b	3	0.41	0.22	0.81	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·Nb

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

Site type: 2O_b·N_b