	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
3hux	A2987	cis-2O_ph·N_b	3	0.15	0.27	0.71	no
3hux	A2990	cis-2O_ph·N_b	3	0.20	0.36	0.39	no
3huz	A2981	cis-2O_ph·N_b	3	0.24	0.31	0.33	no
3huz	B183	cis-2O_ph·N_b	3	0.09	0.35	0.77	no
3huz	A2979	cis-2O_ph·N_b	3	0.22	0.37	0.42	no
3i1n	A3029	cis-2O_ph·N_b	6	0.80	0.82	0.99	yes
3i1p	A3027	cis-2O_ph·N_b	6	0.58	0.57	0.79	no
3i1p	A3024	cis-2O_ph·N_b	6	0.66	0.74	0.92	yes
3i1p	A3022	cis-2O_ph·N_b	6	0.62	0.58	0.73	no
3i1r	A3028	cis-2O_ph·N_b	6	0.77	0.84	0.99	yes
3i1t	A3027	cis-2O_ph·N_b	6	0.59	0.57	0.98	no
3i1t	A3024	cis-2O_ph·N_b	6	0.77	0.83	0.98	yes
3i20	A3028	cis-2O_ph·N_b	6	0.77	0.88	0.99	yes
3i22	A3026	cis-2O_ph·N_b	6	0.55	0.52	1.00	no
3i22	A3021	cis-2O_ph·N_b	6	0.63	0.56	0.99	no
3i22	A3023	cis-2O_ph·N_b	6	0.65	0.65	1.00	yes
3i56	08061	cis-2O_ph·N_b	6	0.54	0.86	0.80	yes
3i56	08068	cis-2O_ph·N_b	5	0.20	0.87	0.71	no
3i8g	A1738	cis-2O_ph·N_b	3	0.18	0.28	0.93	no
3i8h	A2136	cis-2O_ph·N_b	3	0.06	0.61	0.94	no
3i9b	A1590	cis-2O_ph·N_b	3	0.23	0.51	0.86	no
3kir	A2958	cis-2O_ph·N_b	3	0.40	0.29	0.71	no
3kir	A2961	cis-2O_ph·N_b	3	0.35	0.29	0.65	no
3kit	A2958	cis-2O_ph·N_b	3	0.31	0.33	0.78	no
3kit	A2961	cis-2O_ph·N_b	3	0.42	0.37	0.55	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: cis-2Oph·Nb

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

Site type: cis-2O_ph·N_b