MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2935, See in JSmolClick on the image to toggle views Site type: 4Pout·2Bout Schematic drawing for 4Pout·2Bout List of all 45 Mg2+ binding sites with the site type 4Pout·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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vs6 B2935 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qan A2189 4Pout·2Bout 6   0.97   0.99   0.99 yes 2qao B3026 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qba B3181 4Pout·2Bout 6   0.97   0.99   1.00 yes 2qba B3157 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qbc B3026 4Pout·2Bout 6   0.97   0.99   1.00 yes 2qbe B3181 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qbf A1572 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qbi B2931 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qow A1560 4Pout·2Bout 6   0.97   1.00   0.99 yes 2qox B2909 4Pout·2Bout 6   0.97   1.00   1.00 yes 2qoz B2931 4Pout·2Bout 6   0.97   0.99   1.00 yes 2qp1 B2909 4Pout·2Bout 6   0.97   0.99   1.00 yes 2xzm 046 4Pout·2Bout 6   0.12   1.00   1.00 no 2z4m A1573 4Pout·2Bout 6   0.97   1.00   1.00 yes 3df1 A2044 4Pout·2Bout 6   0.97   1.00   1.00 yes 3df3 A2189 4Pout·2Bout 6   0.97   1.00   1.00 yes 3r8s A2960 4Pout·2Bout 6   0.75   0.99   1.00 yes 3r8t A2959 4Pout·2Bout 6   0.75   0.99   1.00 yes 3v25 A3285 4Pout·2Bout 5   0.62   0.81   0.83 yes 3v28 A1752 4Pout·2Bout 6   0.75   0.99   0.85 yes 3v2d A3696 4Pout·2Bout 4   0.51   0.95   0.88 yes 3v2e A1658 4Pout·2Bout 4   0.49   0.63   0.87 no 3v2f A3601 4Pout·2Bout 6   0.76   0.96   0.67 yes 4dhc A3632 4Pout·2Bout 6   0.72   0.96   0.81 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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