MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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" Page 2 of 67 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v25 A3064 2Ob 2   0.04   0.27   0.95 no 1vxm A1666 2Ob 2   0.09   0.11   0.65 no 4lf6 A1676 2Ob 2   0.04   0.37   0.86 no 4qcr A3066 2Ob 2   0.06   0.17   0.98 no 4gas A1669 2Ob 2   0.04   0.19   0.86 no 3pyo A2959 2Ob 2   0.04   0.18   0.52 no 3cce 08075 2Ob 5   0.16   0.56   0.97 no 4nw0 A3071 2Ob 2   0.03   0.16   0.72 no 4khp A1685 2Ob 2   0.07   0.23   0.94 no 4ji7 A1676 2Ob 2   0.03   0.16   0.77 no 3v2d A3075 2Ob 2   0.03   0.46   0.95 no 3huw A80 2Ob 2   0.04   0.15   0.49 no 3uz7 A1853 2Ob 2   0.02   0.18   0.80 no 3pyo A2970 2Ob 2   0.04   0.21   0.78 no 4ji1 A1683 2Ob 2   0.07   0.47   0.70 no 4cr1 A2594 2Ob 2   0.06   0.21   0.90 no 4dv1 A1687 2Ob 4   0.34   0.32   0.44 no 4dv2 A1685 2Ob 2   0.06   0.20   0.97 no 3f1e A5099 2Ob 2   0.03   0.15   0.80 no 3oto A1628 2Ob 2   0.05   0.16   0.76 no 2qex 08097 2Ob 6   0.30   0.72   0.89 no 3t1h A1698 2Ob 2   0.04   0.18   0.03 no 3cc2 08097 2Ob 6   0.42   0.77   0.84 no 2uuc Z1098 2Ob 2   0.09   0.27   0.86 no 3ivn A101 2Ob 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

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout 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].

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