	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
4qcn	A3349	2O_b	3	0.15	0.21	0.90	no
3v22	A1619	2O_b	2	0.04	0.19	0.90	no
1hnx	A1614	2O_b	2	0.07	0.19	0.90	no
3v2f	A3531	2O_b	4	0.27	0.51	0.90	no
3v23	B202	2O_b	2	0.03	0.16	0.90	no
4lfb	A1640	2O_b	2	0.04	0.20	0.90	no
4qcv	A3575	2O_b	4	0.28	0.90	0.90	no
1w2b	38097	2O_b	4	0.14	0.53	0.90	no
4kvb	A1736	2O_b	2	0.32	0.56	0.90	no
3v2f	A3082	2O_b	2	0.04	0.20	0.90	no
4nxm	A1697	2O_b	2	0.04	0.17	0.90	no
1yjn	08097	2O_b	6	0.56	0.49	0.90	no
4qcz	A3354	2O_b	3	0.17	0.28	0.90	no
4qcv	A3188	2O_b	2	0.05	0.54	0.90	no
1jj2	08097	2O_b	6	0.50	0.71	0.90	yes
4dha	B203	2O_b	2	0.04	0.38	0.90	no
3v24	A1627	2O_b	2	0.03	0.17	0.90	no
4tp2	A1655	2O_b	2	0.03	0.21	0.90	no
4qcn	A3225	2O_b	3	0.06	0.45	0.90	no
4kj6	A1603	2O_b	4	0.15	0.76	0.90	no
3pyo	A3232	2O_b	2	0.04	0.30	0.90	no
1qvf	08042	2O_b	6	0.31	0.80	0.90	no
3u5h	53834	2O_b	2	0.04	0.21	0.90	no
4qcy	A3090	2O_b	2	0.08	0.18	0.90	no
4kx0	A3163	2O_b	2	0.13	0.35	0.90	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