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 17 of 19 | « Previous | Next » | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4ji1 A1779 2Pout·2Bout 6   0.96   0.99   0.33 no 4ji6 A1810 2Pout·2Bout 6   0.96   0.99   0.42 no 1vs8 B2907 2Pout·2Bout 6   0.97   1.00   1.00 yes 1vs6 B3001 2Pout·2Bout 6   0.97   0.98   1.00 yes 4ji7 A1859 2Pout·2Bout 6   0.97   0.98   0.72 yes 3df3 A2346 2Pout·2Bout 6   0.97   1.00   1.00 yes 1vs5 A1600 2Pout·2Bout 6   0.97   1.00   1.00 yes 4ji5 A1702 2Pout·2Bout 6   0.97   0.99   0.64 yes 2z4l B2998 2Pout·2Bout 6   0.97   1.00   1.00 yes 2qbi B3001 2Pout·2Bout 6   0.97   0.99   1.00 yes 2aw7 A1565 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qbj A1546 2Pout·2Bout 6   0.97   1.00   1.00 yes 2avy A1599 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qan A2353 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qp1 B2917 2Pout·2Bout 6   0.97   0.99   1.00 yes 2z4n B2963 2Pout·2Bout 6   0.97   1.00   1.00 yes 2i2v B3016 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qoy A1545 2Pout·2Bout 6   0.97   0.99   1.00 yes 2i2p A1598 2Pout·2Bout 6   0.97   1.00   1.00 yes 2qb9 A2077 2Pout·2Bout 6   0.97   1.00   1.00 yes 2qbe B3521 2Pout·2Bout 6   0.97   1.00   0.50 yes 2aw4 B3001 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qoz B3001 2Pout·2Bout 6   0.97   0.99   1.00 yes 3df1 A2150 2Pout·2Bout 6   0.97   1.00   1.00 yes 2qan A2346 2Pout·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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