MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4ji1:A1760, See in JSmolClick on the image to toggle views Site type: 3Pout·2Rout Schematic drawing for 3Pout·2Rout List of all 14 Mg2+ binding sites with the site type 3Pout·2Rout 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 2g3s C1602 3Pout·2Rout 6   0.98   0.95   0.18 no 3i22 A2978 3Pout·2Rout 5   0.81   0.81   1.00 yes 3oxb A111 3Pout·2Rout 5   0.62   0.80   0.57 yes 3v2d A3149 3Pout·2Rout 5   0.65   0.82   0.84 yes 4bpe A5003 3Pout·2Rout 6   0.74   1.00   1.00 yes 4bpn A5003 3Pout·2Rout 6   0.74   0.99   1.00 yes 4bpo A5064 3Pout·2Rout 6   0.76   0.99   1.00 yes 4bpp A5003 3Pout·2Rout 6   0.75   1.00   1.00 yes 4duy A1789 3Pout·2Rout 6   0.96   0.99   0.65 yes 4ji1 A1760 3Pout·2Rout 6   0.95   0.99   0.99 yes 4ji5 A1697 3Pout·2Rout 6   0.96   0.97   0.51 yes 4ji5 A1704 3Pout·2Rout 6   0.98   0.99   0.30 no 4ji7 A1824 3Pout·2Rout 6   0.95   0.98   0.51 yes 4ji8 A1862 3Pout·2Rout 6   0.91   0.97   0.31 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/)
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