MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 277 Mg2+ binding sites with the site type 2Pout·3Bout 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 9 of 12 | « 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 4ji5 A1716 2Pout·3Bout 6   0.95   0.98   0.30 no 4ji5 A1700 2Pout·3Bout 6   0.97   0.99   0.75 yes 4ji6 A1763 2Pout·3Bout 6   0.93   0.99   0.42 no 4ji6 A1812 2Pout·3Bout 6   0.90   0.98   0.19 no 4ji6 A1819 2Pout·3Bout 6   0.95   0.97   0.37 no 4ji6 A1803 2Pout·3Bout 6   0.97   0.95   0.99 yes 4ji6 A1897 2Pout·3Bout 6   0.92   0.98   0.33 no 4ji7 A2013 2Pout·3Bout 6   0.98   0.95   0.31 no 4ji7 A1861 2Pout·3Bout 6   0.95   0.99   0.25 no 4ji7 A1850 2Pout·3Bout 6   0.96   0.99   0.72 yes 4ji7 A1981 2Pout·3Bout 6   0.93   0.96   0.23 no 4ji8 A1915 2Pout·3Bout 6   0.90   0.94   0.34 no 4ji8 A1832 2Pout·3Bout 6   0.96   0.95   0.60 yes 4ji8 A1952 2Pout·3Bout 6   0.87   0.94   0.28 no 4ji8 A1884 2Pout·3Bout 6   0.90   0.96   0.34 no 4kiy A1635 2Pout·3Bout 3   0.19   0.24   0.50 no 4kiy A1631 2Pout·3Bout 3   0.43   0.36   0.82 no 4kiz A3081 2Pout·3Bout 4   0.42   0.29   0.88 no 4kj2 A1613 2Pout·3Bout 3   0.43   0.16   0.82 no 4kj5 A3002 2Pout·3Bout 3   0.32   0.36   0.68 no 4kj5 A3017 2Pout·3Bout 5   0.80   0.51   0.21 no 4kj9 A3002 2Pout·3Bout 3   0.90   0.61   0.96 no 4kjb A3002 2Pout·3Bout 5   0.32   0.41   0.98 no 4nvw A3163 2Pout·3Bout 2   0.25   0.96   0.85 no 4nvw A3168 2Pout·3Bout 3   0.38   0.66   1.00 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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