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 12 of 19 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3r8s A3035 2Pout·2Bout 6   0.71   0.97   1.00 yes 3oat A3036 2Pout·2Bout 6   0.75   0.98   0.43 no 3ofz A3036 2Pout·2Bout 6   0.75   0.99   0.37 no 3i1r A3036 2Pout·2Bout 6   0.74   1.00   1.00 yes 3ofr A3036 2Pout·2Bout 6   0.75   0.99   0.62 yes 3r8s A3037 2Pout·2Bout 6   0.72   0.97   1.00 yes 3i20 A3038 2Pout·2Bout 6   0.74   0.99   1.00 yes 3i1r A3038 2Pout·2Bout 6   0.74   0.99   1.00 yes 3i1n A3039 2Pout·2Bout 6   0.74   1.00   0.42 no 4kj1 A3056 2Pout·2Bout 4   0.67   0.32   0.33 no 4too A3062 2Pout·2Bout 6   0.73   0.98   0.77 yes 4gau A3068 2Pout·2Bout 6   0.75   1.00   0.79 yes 4gar A3069 2Pout·2Bout 6   0.75   1.00   0.75 yes 4kj1 A3074 2Pout·2Bout 3   0.64   0.24   0.33 no 4too A3082 2Pout·2Bout 6   0.74   0.99   0.75 yes 4gar A3083 2Pout·2Bout 6   0.75   1.00   0.88 yes 4tox A3083 2Pout·2Bout 6   0.74   0.98   0.80 yes 4tp7 A3083 2Pout·2Bout 6   0.74   0.99   0.92 yes 4pec A3084 2Pout·2Bout 6   0.74   0.99   0.86 yes 4peb A3084 2Pout·2Bout 6   0.74   0.97   1.00 yes 4tp3 A3085 2Pout·2Bout 6   0.74   1.00   0.83 yes 4tp1 A3086 2Pout·2Bout 6   0.74   0.99   0.34 no 4tox A3086 2Pout·2Bout 6   0.74   0.98   0.84 yes 4tov A3086 2Pout·2Bout 6   0.73   0.96   0.75 yes 4tp7 A3086 2Pout·2Bout 6   0.74   0.99   0.76 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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