	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
1q7y	A8079	cis-2O_ph·N_b	6	0.04	0.66	0.81	no
4qcn	A3012	cis-2O_ph·N_b	3	0.05	0.66	0.82	no
4ji0	A1667	cis-2O_ph·N_b	3	0.05	0.64	0.95	no
4l6j	A5835	cis-2O_ph·N_b	3	0.05	0.65	0.67	no
2uxc	Z69	cis-2O_ph·N_b	3	0.06	0.70	0.86	no
4dr3	A1665	cis-2O_ph·N_b	3	0.06	0.54	0.96	no
3i8h	A2136	cis-2O_ph·N_b	3	0.06	0.61	0.94	no
2uu9	Z1135	cis-2O_ph·N_b	3	0.06	0.75	0.79	no
3d5b	A3299	cis-2O_ph·N_b	3	0.06	0.41	0.14	no
2j02	Z183	cis-2O_ph·N_b	3	0.06	0.69	0.68	no
3d5d	A3492	cis-2O_ph·N_b	3	0.06	0.67	0.33	no
4nvz	A3037	cis-2O_ph·N_b	3	0.06	0.45	0.56	no
4qd1	A3015	cis-2O_ph·N_b	3	0.06	0.58	0.68	no
3d5b	A3225	cis-2O_ph·N_b	3	0.07	0.77	0.26	no
4dv5	A1651	cis-2O_ph·N_b	3	0.07	0.58	0.95	no
4nvv	A3037	cis-2O_ph·N_b	4	0.07	0.68	0.70	no
3v26	A1612	cis-2O_ph·N_b	3	0.07	0.35	0.70	no
3uz3	A1873	cis-2O_ph·N_b	3	0.07	0.49	0.73	no
3oh5	A3094	cis-2O_ph·N_b	3	0.07	0.39	0.52	no
3oh7	A101	cis-2O_ph·N_b	3	0.07	0.27	0.97	no
4dhb	A1710	cis-2O_ph·N_b	3	0.08	0.67	0.88	no
4g5k	A1679	cis-2O_ph·N_b	3	0.08	0.43	0.77	no
4qcw	A3078	cis-2O_ph·N_b	3	0.08	0.42	0.82	no
3d5b	A3136	cis-2O_ph·N_b	3	0.09	0.18	0.18	no
3sgf	A2992	cis-2O_ph·N_b	3	0.09	0.64	0.56	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