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 8 of 67 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3sgf A3214 2Ob 2   0.07   0.36   0.44 no 2uuc Z1167 2Ob 2   0.25   0.05   0.53 no 3i9d A1815 2Ob 2   0.04   0.20   0.78 no 4dr5 A1767 2Ob 2   0.04   0.21   0.67 no 3hux A2916 2Ob 2   0.06   0.13   0.47 no 3ohk A3202 2Ob 2   0.03   0.19   0.89 no 4l6j A4725 2Ob 2   0.03   0.17   0.54 no 3oh7 A163 2Ob 2   0.06   0.25   0.99 no 3sgf A3235 2Ob 2   0.04   0.21   0.99 no 4dr6 A1931 2Ob 2   0.04   0.14   0.82 no 3ohz A166 2Ob 2   0.03   0.20   0.80 no 4ji6 A1934 2Ob 2   0.08   0.16   0.99 no 3ohz A3214 2Ob 2   0.05   0.20   1.00 no 4dr6 A1934 2Ob 2   0.03   0.18   0.97 no 3oi3 A3208 2Ob 2   0.09   0.16   0.77 no 3u5f 62149 2Ob 2   0.03   0.22   0.90 no 4dhc A3347 2Ob 2   0.03   0.19   0.90 no 3t1h A1698 2Ob 2   0.04   0.18   0.03 no 4nw0 A3019 2Ob 2   0.07   0.24   0.68 no 3r8s A3073 2Ob 2   0.05   0.18   0.01 no 3v2d A3352 2Ob 2   0.03   0.17   0.69 no 4ji6 A1957 2Ob 2   0.04   0.19   0.84 no 4tp5 A3174 2Ob 2   0.04   0.18   0.61 no 4qcr A3171 2Ob 2   0.06   0.21   0.91 no 3u5d 14055 2Ob 2   0.05   0.19   0.97 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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