MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qam:B3090, See in JSmolClick on the image to toggle views Site type: Oph·2Pout Schematic drawing for Oph·2Pout List of all 2450 Mg2+ binding sites with the site type Oph·2Pout 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 98 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1dul B803 Oph·2Pout 6   0.91   0.89   0.60 yes 1dul B802 Oph·2Pout 6   0.87   0.86   0.83 yes 1f27 A36 Oph·2Pout 6   0.97   0.93   0.89 yes 1feu F324 Oph·2Pout 6   0.91   0.86   0.82 yes 1ffy T1205 Oph·2Pout 5   0.55   0.72   0.94 yes 1hq1 B1802 Oph·2Pout 6   0.95   0.81   0.99 yes 1jj2 08083 Oph·2Pout 6   0.85   0.84   0.98 yes 1jj2 08082 Oph·2Pout 5   0.27   0.42   0.62 no 1jj2 08036 Oph·2Pout 6   0.90   0.93   0.86 yes 1jj2 08092 Oph·2Pout 4   0.47   0.74   0.51 no 1jj2 08068 Oph·2Pout 6   0.66   0.87   0.99 yes 1jj2 08020 Oph·2Pout 6   0.79   0.93   0.76 yes 1jj2 08045 Oph·2Pout 5   0.50   0.72   0.89 yes 1jj2 08019 Oph·2Pout 6   0.90   0.79   0.76 yes 1k73 A8083 Oph·2Pout 6   0.79   0.89   0.83 yes 1k73 A8019 Oph·2Pout 6   0.92   0.71   0.74 yes 1k73 A8036 Oph·2Pout 6   0.38   0.74   0.65 no 1k73 A8045 Oph·2Pout 5   0.53   0.63   0.98 yes 1k73 A8068 Oph·2Pout 6   0.76   0.75   0.93 yes 1k73 A8092 Oph·2Pout 4   0.61   0.75   0.61 yes 1k73 A8020 Oph·2Pout 6   0.41   0.79   0.73 no 1k8a A8036 Oph·2Pout 6   0.54   0.90   0.49 no 1k8a A8020 Oph·2Pout 6   0.57   0.88   0.94 yes 1k8a A8083 Oph·2Pout 6   0.87   0.88   0.96 yes 1k8a A8092 Oph·2Pout 4   0.80   0.76   0.49 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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