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 13 of 19 | « Previous | Next » | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv6 A1831 2Pout·2Bout 4   0.64   0.63   0.58 yes 4dr7 A1831 2Pout·2Bout 6   0.93   0.98   0.23 no 4dv4 A1830 2Pout·2Bout 6   0.91   0.98   0.36 no 4ji7 A1829 2Pout·2Bout 6   0.94   0.99   0.32 no 4dv1 A1828 2Pout·2Bout 4   0.61   0.69   0.33 no 4dhb A1827 2Pout·2Bout 4   0.49   0.98   0.81 no 4dv1 A1827 2Pout·2Bout 6   0.95   0.99   0.41 no 4dv6 A1825 2Pout·2Bout 6   0.95   0.99   0.45 no 4duy A1824 2Pout·2Bout 4   0.65   0.64   0.75 yes 4dr5 A1823 2Pout·2Bout 6   0.96   1.00   0.42 no 4dr5 A1822 2Pout·2Bout 6   0.95   0.99   0.58 yes 4duz A1820 2Pout·2Bout 5   0.79   0.77   0.82 yes 4dv5 A1820 2Pout·2Bout 5   0.76   0.83   0.31 no 4duy A1817 2Pout·2Bout 6   0.95   1.00   0.48 no 4dv6 A1813 2Pout·2Bout 4   0.63   0.65   0.67 yes 4dr1 A1813 2Pout·2Bout 4   0.63   0.65   0.45 no 3v2c A1811 2Pout·2Bout 6   0.77   0.97   0.99 yes 4ji6 A1810 2Pout·2Bout 6   0.96   0.99   0.42 no 4ji2 A1806 2Pout·2Bout 4   0.62   0.64   0.37 no 4ji6 A1805 2Pout·2Bout 6   0.89   0.97   0.30 no 4dv6 A1805 2Pout·2Bout 4   0.64   0.64   0.44 no 4ji1 A1804 2Pout·2Bout 6   0.91   0.89   0.40 no 4dr3 A1802 2Pout·2Bout 4   0.64   0.64   0.66 yes 4ji1 A1802 2Pout·2Bout 6   0.96   0.99   0.50 yes 4duy A1794 2Pout·2Bout 5   0.79   0.80   0.36 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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