	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
4nw1	A3180	cis-2O_ph·N_b	3	0.40	0.23	0.89	no
4kjb	A3123	cis-2O_ph·N_b	4	0.43	0.47	0.75	no
4qct	A3471	cis-2O_ph·N_b	5	0.36	0.50	0.79	no
4qcm	A1696	cis-2O_ph·N_b	3	0.14	0.32	0.84	no
4nvx	A3182	cis-2O_ph·N_b	3	0.26	0.31	0.72	no
4kjb	A3077	cis-2O_ph·N_b	6	0.26	0.60	0.82	no
4tp5	A3126	cis-2O_ph·N_b	6	0.84	0.85	0.20	no
1vy1	A3053	cis-2O_ph·N_b	3	0.42	0.40	0.07	no
4qcp	A3463	cis-2O_ph·N_b	5	0.34	0.49	0.69	no
4qcn	A3012	cis-2O_ph·N_b	3	0.05	0.66	0.82	no
4tp9	A3129	cis-2O_ph·N_b	6	0.70	0.69	0.42	no
4nw0	A3104	cis-2O_ph·N_b	4	0.19	0.30	0.82	no
4nvw	A3104	cis-2O_ph·N_b	4	0.17	0.26	0.97	no
4kx2	A3063	cis-2O_ph·N_b	3	0.44	0.34	0.14	no
4qd1	A3015	cis-2O_ph·N_b	3	0.06	0.58	0.68	no
4qd1	A3181	cis-2O_ph·N_b	3	0.36	0.27	0.74	no
4qd1	A3261	cis-2O_ph·N_b	3	0.29	0.34	0.83	no
4tp5	A3129	cis-2O_ph·N_b	6	0.84	0.90	0.43	no
4qcz	A3578	cis-2O_ph·N_b	4	0.22	0.39	0.99	no
4qcx	A3165	cis-2O_ph·N_b	3	0.23	0.30	0.87	no
4qcx	A3202	cis-2O_ph·N_b	3	0.33	0.32	0.69	no
4qcw	A3078	cis-2O_ph·N_b	3	0.08	0.42	0.82	no
4qcv	A3215	cis-2O_ph·N_b	3	0.35	0.32	0.82	no
4qct	A3191	cis-2O_ph·N_b	3	0.25	0.21	0.94	no
4kja	A1617	cis-2O_ph·N_b	4	0.41	0.35	0.51	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