	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
3cpw	08032	2O_b	6	0.28	0.83	0.79	no
3g4s	08032	2O_b	4	0.12	0.69	0.96	no
1vvt	A1632	2O_b	2	0.07	0.23	0.41	no
3cce	08032	2O_b	5	0.22	0.71	0.96	no
3ccv	08032	2O_b	6	0.20	0.82	0.76	no
3ccl	08032	2O_b	6	0.18	0.79	0.97	no
3cc4	08032	2O_b	6	0.18	0.86	0.91	no
3ccr	08032	2O_b	5	0.11	0.56	0.84	no
3g6e	08032	2O_b	6	0.19	0.92	0.97	no
3ccq	08032	2O_b	6	0.22	0.85	0.92	no
1vqm	08042	2O_b	6	0.29	0.73	0.81	no
4tp2	A1635	2O_b	4	0.37	0.42	0.98	no
4gd2	A1635	2O_b	4	0.43	0.51	0.65	no
4byb	A2566	2O_b	2	0.15	0.29	0.99	no
2qoy	A1577	2O_b	4	0.37	0.45	0.97	no
4qcv	A3036	2O_b	2	0.06	0.13	0.90	no
4gkj	A1640	2O_b	2	0.20	0.40	0.99	no
3knj	A1569	2O_b	2	0.04	0.13	0.57	no
4duy	A1639	2O_b	4	0.36	0.39	0.53	no
4nvv	A3038	2O_b	2	0.04	0.20	0.75	no
4nvz	A3038	2O_b	2	0.03	0.23	0.61	no
4dr4	A1656	2O_b	4	0.35	0.44	0.98	no
4nw1	A3039	2O_b	2	0.06	0.16	0.79	no
2uua	Z58	2O_b	2	0.07	0.23	0.78	no
3ivn	A101	2O_b	2	0.03	0.17	0.91	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