	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 2r8s:R1004, See in JSmol MgRNA representative site for type 2OB

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Site type: 2O_b

Schematic drawing for
2O_b
MgRNA type 2OB

List of all 1662 Mg²⁺ binding sites with the site type 2O_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
1ibm	A1656	2O_b	2	0.06	0.16	0.71	no
1ibm	A210	2O_b	2	0.06	0.17	0.55	no
1ibm	A1611	2O_b	2	0.06	0.17	0.68	no
1ibm	A1616	2O_b	2	0.03	0.26	0.35	no
1jid	B302	2O_b	6	0.36	0.85	0.85	no
1jj2	08042	2O_b	6	0.34	0.96	0.95	no
1jj2	08097	2O_b	6	0.50	0.71	0.90	yes
1k73	A8042	2O_b	6	0.35	0.86	0.84	no
1k73	A8097	2O_b	6	0.44	0.73	0.87	no
1k8a	A8097	2O_b	6	0.35	0.87	0.71	no
1k8a	A8042	2O_b	5	0.40	0.57	0.89	no
1k9m	A8097	2O_b	6	0.37	0.80	0.91	no
1k9m	A8042	2O_b	6	0.44	0.56	0.84	no
1kc8	A8097	2O_b	6	0.49	0.66	0.98	no
1kc8	A8042	2O_b	6	0.31	0.79	0.90	no
1kd1	A8097	2O_b	6	0.46	0.75	0.85	no
1kd1	A8042	2O_b	6	0.38	0.58	0.93	no
1kqs	08042	2O_b	6	0.23	0.86	0.79	no
1kqs	08097	2O_b	6	0.41	0.90	0.85	no
1m1k	A8042	2O_b	6	0.33	0.79	0.94	no
1m1k	A8097	2O_b	6	0.39	0.84	0.95	no
1m90	A8097	2O_b	6	0.42	0.82	0.99	no
1m90	A8042	2O_b	6	0.27	0.88	0.88	no
1n32	A1667	2O_b	2	0.05	0.21	0.50	no
1n32	A1609	2O_b	2	0.08	0.16	0.47	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: 2Ob

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

Site type: 2O_b