	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
2xfz	Z1646	cis-2O_ph·N_b	3	0.30	0.16	0.53	no
3d5b	A3136	cis-2O_ph·N_b	3	0.09	0.18	0.18	no
1vy3	A3040	cis-2O_ph·N_b	3	0.26	0.19	0.89	no
3ohk	A2985	cis-2O_ph·N_b	3	0.20	0.19	0.90	no
4kj5	A3020	cis-2O_ph·N_b	5	0.51	0.20	0.29	no
3kni	A3199	cis-2O_ph·N_b	3	0.36	0.21	0.86	no
4qct	A3191	cis-2O_ph·N_b	3	0.25	0.21	0.94	no
3oi5	A2984	cis-2O_ph·N_b	3	0.19	0.21	0.95	no
1vxl	A3195	cis-2O_ph·N_b	3	0.39	0.22	0.67	no
3kni	A2974	cis-2O_ph·N_b	3	0.32	0.22	0.39	no
3kno	A2961	cis-2O_ph·N_b	3	0.30	0.22	0.05	no
3oi1	A2982	cis-2O_ph·N_b	3	0.17	0.22	0.98	no
4nw1	A3180	cis-2O_ph·N_b	3	0.40	0.23	0.89	no
3oi3	A2982	cis-2O_ph·N_b	3	0.16	0.23	0.67	no
1vvw	A3039	cis-2O_ph·N_b	3	0.54	0.23	0.02	no
4dhc	A3107	cis-2O_ph·N_b	3	0.14	0.24	0.77	no
3sgf	A2972	cis-2O_ph·N_b	3	0.15	0.24	0.69	no
3v23	A3132	cis-2O_ph·N_b	3	0.09	0.24	0.95	no
3oi3	A2985	cis-2O_ph·N_b	3	0.30	0.24	0.86	no
3d5d	A2982	cis-2O_ph·N_b	3	0.13	0.24	0.18	no
3v25	A3251	cis-2O_ph·N_b	3	0.12	0.24	0.89	no
1vxt	A3039	cis-2O_ph·N_b	3	0.48	0.24	0.94	no
4qcp	A3177	cis-2O_ph·N_b	3	0.29	0.25	0.95	no
3ohz	A2984	cis-2O_ph·N_b	3	0.19	0.25	0.67	no
1vvu	A3048	cis-2O_ph·N_b	3	0.51	0.25	0.44	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