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 1 of 19 | « 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 1k73 A8082 2Pout·2Bout 4   0.27   0.45   0.76 no 1kd1 A8082 2Pout·2Bout 4   0.29   0.62   0.81 no 1mms C273 2Pout·2Bout 5   0.33   0.46   0.91 no 1q7y A8093 2Pout·2Bout 4   0.16   0.40   0.37 no 1vqk 08082 2Pout·2Bout 3   0.09   0.25   0.70 no 1vqo 08082 2Pout·2Bout 3   0.07   0.36   0.65 no 1vs5 A1600 2Pout·2Bout 6   0.97   1.00   1.00 yes 1vs6 B3001 2Pout·2Bout 6   0.97   0.98   1.00 yes 1vs6 B2937 2Pout·2Bout 6   0.97   0.99   1.00 yes 1vs6 B2957 2Pout·2Bout 6   0.98   0.99   1.00 yes 1vs7 A1566 2Pout·2Bout 6   0.97   1.00   1.00 yes 1vs8 B2907 2Pout·2Bout 6   0.97   1.00   1.00 yes 1vt2 A2921 2Pout·2Bout 6   0.75   1.00   0.88 yes 1vt2 A3033 2Pout·2Bout 6   0.73   0.97   0.39 no 1yj9 08098 2Pout·2Bout 4   0.23   0.48   0.69 no 1yjn 08100 2Pout·2Bout 6   0.62   0.62   0.74 yes 1yls B242 2Pout·2Bout 6   0.81   0.99   1.00 yes 2avy A1599 2Pout·2Bout 6   0.97   0.99   1.00 yes 2aw4 B3001 2Pout·2Bout 6   0.97   0.99   1.00 yes 2aw4 B2937 2Pout·2Bout 6   0.97   0.99   1.00 yes 2aw7 A1565 2Pout·2Bout 6   0.97   0.99   1.00 yes 2i2p A1550 2Pout·2Bout 6   0.97   1.00   1.00 yes 2i2p A1598 2Pout·2Bout 6   0.97   1.00   1.00 yes 2i2u A1581 2Pout·2Bout 5   0.81   0.80   1.00 yes 2i2v B3016 2Pout·2Bout 6   0.97   0.99   1.00 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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