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 4 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 4dr7 A1741 2Ob 2   0.08   0.18   0.67 no 3uz7 A1971 2Ob 2   0.04   0.16   0.85 no 2wdg Z230 2Ob 2   0.02   0.18   0.99 no 2wdg Z234 2Ob 2   0.08   0.16   0.66 no 4dr1 A1748 2Ob 2   0.04   0.15   0.83 no 4eja A7171 2Ob 2   0.02   0.16   0.80 no 2wdg Z237 2Ob 2   0.04   0.22   0.89 no 3v27 A3154 2Ob 2   0.03   0.14   0.94 no 3pyt A3005 2Ob 2   0.07   0.19   0.65 no 3hux A156 2Ob 2   0.04   0.22   0.78 no 1fjg A1549 2Ob 2   0.04   0.18   0.84 no 4ji2 A1757 2Ob 2   0.03   0.32   0.71 no 2uuc Z1167 2Ob 2   0.25   0.05   0.53 no 4dr5 A1767 2Ob 2   0.04   0.21   0.67 no 3f1e A5099 2Ob 2   0.03   0.15   0.80 no 3oh7 A163 2Ob 2   0.06   0.25   0.99 no 3ohz A166 2Ob 2   0.03   0.20   0.80 no 3kiy A3055 2Ob 2   0.06   0.19   0.94 no 3mrz A2940 2Ob 2   0.03   0.15   0.79 no 3v23 A3166 2Ob 2   0.03   0.18   0.97 no 3t1h A1698 2Ob 2   0.04   0.18   0.03 no 3r8s A3073 2Ob 2   0.05   0.18   0.01 no 4tp5 A3174 2Ob 2   0.04   0.18   0.61 no 4qcr A3171 2Ob 2   0.06   0.21   0.91 no 1vy1 A3196 2Ob 2   0.08   0.22   0.76 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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