	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 2qou:A1560, See in JSmol MgRNA representative site for type NB

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Site type: N_b

Schematic drawing for
N_b
MgRNA type NB

List of all 2195 Mg²⁺ binding sites with the site type 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
1vq7	08114	N_b	6	0.29	0.95	0.69	no
1vq7	08046	N_b	4	0.35	0.63	0.91	no
1vq7	08098	N_b	6	0.32	0.91	0.86	no
1vq7	08111	N_b	6	0.45	0.87	0.97	no
1vq8	08112	N_b	6	0.46	0.79	0.91	no
1vq8	08113	N_b	6	0.33	0.84	0.74	no
1vq8	08114	N_b	5	0.30	0.88	0.80	no
1vq8	08046	N_b	4	0.32	0.66	0.76	no
1vq8	08068	N_b	6	0.34	0.72	0.61	no
1vq8	08098	N_b	6	0.33	0.90	0.78	no
1vq9	08068	N_b	5	0.57	0.85	0.55	yes
1vq9	08112	N_b	6	0.47	0.83	0.89	no
1vq9	08098	N_b	6	0.28	0.85	0.84	no
1vq9	08114	N_b	4	0.16	0.22	0.86	no
1vq9	08046	N_b	3	0.28	0.34	0.79	no
1vq9	08089	N_b	2	0.03	0.65	0.91	no
1vqk	08068	N_b	6	0.58	0.86	0.56	yes
1vqk	08113	N_b	6	0.32	0.87	0.88	no
1vqk	08098	N_b	6	0.34	0.80	0.88	no
1vqk	08112	N_b	6	0.47	0.81	0.94	no
1vqk	08114	N_b	5	0.22	0.63	0.91	no
1vqk	08046	N_b	4	0.26	0.56	0.78	no
1vql	08114	N_b	5	0.30	0.75	0.93	no
1vql	08098	N_b	6	0.36	0.85	0.80	no
1vql	08024	N_b	2	0.18	0.19	0.74	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: Nb

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

Site type: N_b