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 9 of 19 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4tpe A1620 2Pout·2Bout 6   0.75   0.99   0.89 yes 3ofr A3036 2Pout·2Bout 6   0.75   0.99   0.62 yes 3i1t A3033 2Pout·2Bout 6   0.74   0.99   1.00 yes 4gau A3130 2Pout·2Bout 6   0.75   1.00   0.96 yes 3ofq A2922 2Pout·2Bout 6   0.75   1.00   0.96 yes 1vt2 A2921 2Pout·2Bout 6   0.75   1.00   0.88 yes 3or9 A1535 2Pout·2Bout 6   0.74   0.99   0.48 no 3r8s A3023 2Pout·2Bout 6   0.75   0.97   1.00 yes 3oar A1549 2Pout·2Bout 6   0.75   1.00   0.96 yes 3r8s A3035 2Pout·2Bout 6   0.71   0.97   1.00 yes 3i20 A3022 2Pout·2Bout 6   0.75   0.99   1.00 yes 4too A3134 2Pout·2Bout 6   0.73   0.99   0.63 yes 3i1r A3022 2Pout·2Bout 6   0.75   0.99   1.00 yes 4too A3016 2Pout·2Bout 6   0.73   0.98   0.63 yes 3r8t A3022 2Pout·2Bout 6   0.73   0.99   0.99 yes 4tpf A3120 2Pout·2Bout 6   0.74   1.00   0.74 yes 4peb A3119 2Pout·2Bout 6   0.74   0.97   0.81 yes 3v2c A1811 2Pout·2Bout 6   0.77   0.97   0.99 yes 4pec A3119 2Pout·2Bout 6   0.73   0.99   0.77 yes 2qb9 A2077 2Pout·2Bout 6   0.97   1.00   1.00 yes 4dr5 A1834 2Pout·2Bout 6   0.95   1.00   0.64 yes 4dv7 A1870 2Pout·2Bout 6   0.96   0.99   0.52 yes 4ji6 A1887 2Pout·2Bout 6   0.97   0.98   0.87 yes 4tp5 A3120 2Pout·2Bout 6   0.74   0.98   0.52 yes 4tox A3120 2Pout·2Bout 6   0.73   0.99   0.70 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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