MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2aw4:B2955, See in JSmolClick on the image to toggle views Site type: 4Pout·Rout Schematic drawing for 4Pout·Rout List of all 62 Mg2+ binding sites with the site type 4Pout·Rout 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 2 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3i21 A1570 4Pout·Rout 5   0.80   0.82   1.00 yes 3oar A1572 4Pout·Rout 5   0.82   0.80   0.61 yes 3oas A3022 4Pout·Rout 4   0.67   0.99   0.92 yes 3og0 A2996 4Pout·Rout 6   0.75   0.99   0.98 yes 3oxd B132 4Pout·Rout 6   0.75   1.00   0.71 yes 3r8s A2918 4Pout·Rout 6   0.72   0.98   1.00 yes 3v28 A1757 4Pout·Rout 4   0.49   0.97   0.84 no 3v2f A3368 4Pout·Rout 5   0.61   0.82   0.70 yes 4bpe A5050 4Pout·Rout 6   0.75   0.98   1.00 yes 4bpo A5037 4Pout·Rout 6   0.74   1.00   0.99 yes 4bpo A5050 4Pout·Rout 6   0.75   0.99   1.00 yes 4bpp A5050 4Pout·Rout 6   0.76   0.98   1.00 yes 4duy A1846 4Pout·Rout 6   0.96   0.99   0.76 yes 4duz A1828 4Pout·Rout 5   0.79   0.80   0.41 no 4dv2 A1834 4Pout·Rout 5   0.82   0.79   0.81 yes 4dv4 A1635 4Pout·Rout 4   0.65   0.66   0.66 yes 4dv6 A1637 4Pout·Rout 4   0.64   0.65   0.62 yes 4dv6 A1856 4Pout·Rout 4   0.64   0.64   0.39 no 4gar A3103 4Pout·Rout 3   0.51   0.42   0.84 no 4gas A1629 4Pout·Rout 4   0.67   0.65   0.83 yes 4gau A3101 4Pout·Rout 3   0.50   0.42   0.93 no 4gau A3057 4Pout·Rout 5   0.82   0.80   0.77 yes 4gd1 A1640 4Pout·Rout 6   0.73   0.98   1.00 yes 4gd2 A1615 4Pout·Rout 6   0.71   0.98   1.00 yes 4ji1 A1810 4Pout·Rout 6   0.96   0.99   0.93 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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