MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 179 Mg2+ binding sites with the site type 3Pout·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 1 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1dfu N504 3Pout·2Bout 6   0.95   0.87   0.63 yes 1l2x A38 3Pout·2Bout 6   0.93   0.99   0.91 yes 1nji A8082 3Pout·2Bout 4   0.42   0.23   0.67 no 1vs6 B2953 3Pout·2Bout 6   0.97   1.00   1.00 yes 1vs6 B2931 3Pout·2Bout 6   0.97   0.99   1.00 yes 1vs7 A1602 3Pout·2Bout 6   0.97   1.00   1.00 yes 1vs8 B2985 3Pout·2Bout 6   0.97   0.99   1.00 yes 1vt2 A2968 3Pout·2Bout 6   0.74   0.99   0.52 yes 1w2b 03975 3Pout·2Bout 5   0.26   0.76   0.93 no 2aw4 B2953 3Pout·2Bout 6   0.97   0.99   1.00 yes 2aw7 A1601 3Pout·2Bout 6   0.97   0.99   1.00 yes 2awb B2907 3Pout·2Bout 6   0.97   1.00   1.00 yes 2awb B2986 3Pout·2Bout 6   0.97   0.99   1.00 yes 2i2t B2953 3Pout·2Bout 6   0.97   1.00   1.00 yes 2i2u A1574 3Pout·2Bout 6   0.97   0.99   1.00 yes 2i2u A1596 3Pout·2Bout 6   0.97   1.00   1.00 yes 2i2v B2907 3Pout·2Bout 6   0.97   0.99   1.00 yes 2i2v B2909 3Pout·2Bout 6   0.97   0.99   1.00 yes 2qal A2044 3Pout·2Bout 6   0.97   1.00   1.00 yes 2qam B3282 3Pout·2Bout 6   0.97   0.99   1.00 yes 2qam B3157 3Pout·2Bout 6   0.97   0.99   1.00 yes 2qao B3014 3Pout·2Bout 6   0.97   1.00   1.00 yes 2qba B3282 3Pout·2Bout 6   0.97   0.99   1.00 yes 2qbc B3014 3Pout·2Bout 6   0.97   1.00   1.00 yes 2qbd A2328 3Pout·2Bout 6   0.97   1.00   1.00 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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