MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 453 Mg2+ binding sites with the site type 2Pout·2Bout 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 6 of 19 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4duy A1794 2Pout·2Bout 5   0.79   0.80   0.36 no 3ofq A2953 2Pout·2Bout 5   0.82   0.80   0.72 yes 3ofq A2918 2Pout·2Bout 5   0.81   0.80   0.71 yes 4qcp A3399 2Pout·2Bout 5   0.62   0.80   0.88 yes 2qov B2946 2Pout·2Bout 5   0.81   0.80   1.00 yes 2z4m A1600 2Pout·2Bout 5   0.81   0.80   0.98 yes 2qan A2340 2Pout·2Bout 5   0.81   0.80   0.97 yes 3v2f A3386 2Pout·2Bout 5   0.62   0.80   0.79 yes 3df4 B3351 2Pout·2Bout 5   0.81   0.80   1.00 yes 2i2u A1581 2Pout·2Bout 5   0.81   0.80   1.00 yes 4dv7 A1865 2Pout·2Bout 5   0.79   0.80   0.66 yes 2qp0 A1595 2Pout·2Bout 5   0.81   0.80   1.00 yes 3og0 A3001 2Pout·2Bout 5   0.82   0.80   0.76 yes 4nvv A3404 2Pout·2Bout 5   0.64   0.80   0.99 yes 4qcu A3163 2Pout·2Bout 5   0.63   0.80   0.94 yes 4duy A1858 2Pout·2Bout 5   0.79   0.80   0.47 no 4duz A1847 2Pout·2Bout 5   0.78   0.81   0.27 no 4dv0 A1611 2Pout·2Bout 5   0.78   0.81   0.49 no 3v23 A3369 2Pout·2Bout 5   0.63   0.81   0.92 yes 3ox0 B124 2Pout·2Bout 5   0.63   0.81   0.75 yes 3i22 A3002 2Pout·2Bout 5   0.82   0.81   1.00 yes 4dv5 A1850 2Pout·2Bout 5   0.78   0.82   0.38 no 3i1p A3003 2Pout·2Bout 5   0.81   0.82   0.76 yes 4dv5 A1820 2Pout·2Bout 5   0.76   0.83   0.31 no 4m4o B103 2Pout·2Bout 5   0.68   0.83   0.78 yes

^# 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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