	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 1vs6:B3008, See in JSmol MgRNA representative site for type cis-2OP-NB

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Site type: cis-2O_ph·N_b

Schematic drawing for
cis-2O_ph·N_b
MgRNA type cis-2OP-NB

List of all 337 Mg²⁺ binding sites with the site type cis-2O_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
1jj2	08089	cis-2O_ph·N_b	6	0.58	0.87	0.81	yes
1k73	A8089	cis-2O_ph·N_b	6	0.63	0.94	0.79	yes
1k73	A8079	cis-2O_ph·N_b	6	0.99	0.89	0.66	yes
1k8a	A8079	cis-2O_ph·N_b	6	0.88	0.92	0.57	yes
1k9m	A8089	cis-2O_ph·N_b	6	0.76	0.58	0.99	no
1k9m	A8079	cis-2O_ph·N_b	6	0.81	0.79	0.79	yes
1kc8	A8079	cis-2O_ph·N_b	6	0.99	0.71	0.96	yes
1kc8	A8089	cis-2O_ph·N_b	6	0.83	0.69	0.84	yes
1kd1	A8089	cis-2O_ph·N_b	6	0.67	0.84	0.70	yes
1kd1	A8079	cis-2O_ph·N_b	6	0.83	0.74	0.78	yes
1kqs	08079	cis-2O_ph·N_b	6	0.94	0.89	0.97	yes
1kqs	08089	cis-2O_ph·N_b	6	0.63	0.72	0.82	yes
1m1k	A8089	cis-2O_ph·N_b	6	0.90	0.68	0.99	yes
1m90	A8089	cis-2O_ph·N_b	6	0.63	0.82	0.93	yes
1n8r	A8079	cis-2O_ph·N_b	6	0.80	0.81	0.86	yes
1n8r	A8089	cis-2O_ph·N_b	6	0.87	0.77	0.80	yes
1nji	A8089	cis-2O_ph·N_b	6	0.70	0.64	0.86	yes
1q7y	A8089	cis-2O_ph·N_b	6	0.49	0.84	0.58	no
1q7y	A8079	cis-2O_ph·N_b	6	0.04	0.66	0.81	no
1q81	A8089	cis-2O_ph·N_b	6	0.51	0.69	0.66	yes
1q81	A8079	cis-2O_ph·N_b	6	0.71	0.72	0.63	yes
1q82	A8089	cis-2O_ph·N_b	6	0.83	0.82	0.75	yes
1q82	A8079	cis-2O_ph·N_b	6	0.98	0.83	0.65	yes
1q86	A8079	cis-2O_ph·N_b	6	0.93	0.93	0.93	yes
1q86	A8089	cis-2O_ph·N_b	6	0.61	0.78	0.95	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: cis-2Oph·Nb

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

Site type: cis-2O_ph·N_b