	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 3r8s:A2932, See in JSmol MgRNA representative site for type OP-NB

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Site type: O_ph·N_b

Schematic drawing for
O_ph·N_b
MgRNA type OP-NB

List of all 892 Mg²⁺ binding sites with the site type O_ph·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
1hr2	A58	O_ph·N_b	2	0.07	0.40	0.83	no
1i96	A1537	O_ph·N_b	2	0.08	0.56	0.88	no
1jj2	08110	O_ph·N_b	6	0.52	0.83	0.81	yes
1k73	A8110	O_ph·N_b	6	0.63	0.84	0.54	yes
1k8a	A8110	O_ph·N_b	6	0.72	0.72	0.74	yes
1k9m	A8110	O_ph·N_b	6	0.63	0.81	0.51	yes
1kc8	A8110	O_ph·N_b	6	0.63	0.75	0.69	yes
1kd1	A8110	O_ph·N_b	6	0.83	0.63	0.94	yes
1kqs	08110	O_ph·N_b	6	0.51	0.84	0.82	yes
1lng	B402	O_ph·N_b	5	0.40	0.56	0.98	no
1m1k	A8110	O_ph·N_b	6	0.73	0.64	0.67	yes
1m90	A8110	O_ph·N_b	6	0.47	0.89	1.00	no
1n8r	A8110	O_ph·N_b	6	0.78	0.60	0.34	no
1nji	A8110	O_ph·N_b	6	0.75	0.75	0.82	yes
1o3z	A307	O_ph·N_b	6	0.50	0.92	0.85	yes
1o3z	B306	O_ph·N_b	6	0.77	0.77	0.82	yes
1q7y	A8110	O_ph·N_b	6	0.81	0.72	0.74	yes
1q81	A8110	O_ph·N_b	5	0.60	0.50	0.81	no
1q82	A8110	O_ph·N_b	6	0.56	0.81	0.78	yes
1q86	A8110	O_ph·N_b	5	0.45	0.77	0.85	no
1qvf	08110	O_ph·N_b	6	0.56	0.77	0.58	yes
1qvg	08110	O_ph·N_b	6	0.37	0.85	1.00	no
1s72	08109	O_ph·N_b	6	0.52	0.83	0.83	yes
1vq4	08110	O_ph·N_b	6	0.42	0.91	0.98	no
1vq5	08110	O_ph·N_b	5	0.39	0.78	0.94	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: Oph·Nb

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

Site type: O_ph·N_b