MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3ofz:A2996, See in JSmolClick on the image to toggle views Site type: Pout·2Rout·2Bout Schematic drawing for Pout·2Rout·2Bout List of all 11 Mg2+ binding sites with the site type Pout·2Rout·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 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ccs 08090 Pout·2Rout·2Bout 5   0.12   0.57   0.95 no 3ofz A2996 Pout·2Rout·2Bout 6   0.76   0.99   0.97 yes 3v2c A1721 Pout·2Rout·2Bout 3   0.37   0.42   1.00 no 3v2e A1657 Pout·2Rout·2Bout 4   0.49   0.96   0.85 no 3v2f A3332 Pout·2Rout·2Bout 3   0.38   0.60   0.84 no 4dha A3730 Pout·2Rout·2Bout 4   0.49   0.93   0.71 no 4dr7 A1872 Pout·2Rout·2Bout 6   0.95   0.99   0.54 yes 4dr7 A1792 Pout·2Rout·2Bout 6   0.95   0.99   0.70 yes 4gau A3092 Pout·2Rout·2Bout 6   0.75   1.00   0.93 yes 4ji6 A1894 Pout·2Rout·2Bout 6   0.96   0.96   0.37 no 4nvx A3261 Pout·2Rout·2Bout 4   0.50   0.64   0.92 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>