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 8 of 19 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4nvx A3321 2Pout·2Bout 4   0.51   0.62   0.90 yes 3v24 A1669 2Pout·2Bout 4   0.52   0.98   0.90 yes 4ji1 A1781 2Pout·2Bout 6   0.96   1.00   0.90 yes 3v25 A3399 2Pout·2Bout 4   0.50   0.99   0.90 no 4qcz A3386 2Pout·2Bout 3   0.37   0.42   0.90 no 4dhc A3495 2Pout·2Bout 3   0.37   0.72   0.90 no 4duz A1677 2Pout·2Bout 2   0.32   0.27   0.90 no 4tp8 A1601 2Pout·2Bout 6   0.75   1.00   0.90 yes 4tpe A1620 2Pout·2Bout 6   0.75   0.99   0.89 yes 4dv4 A1632 2Pout·2Bout 3   0.52   0.66   0.89 no 4qcr A3388 2Pout·2Bout 4   0.50   0.99   0.89 no 3v29 A3353 2Pout·2Bout 4   0.51   0.97   0.89 yes 3cul C503 2Pout·2Bout 2   0.48   0.70   0.89 no 1vt2 A2921 2Pout·2Bout 6   0.75   1.00   0.88 yes 4qcp A3399 2Pout·2Bout 5   0.62   0.80   0.88 yes 4kiz 4101 2Pout·2Bout 4   0.49   0.49   0.88 no 4gar A3083 2Pout·2Bout 6   0.75   1.00   0.88 yes 3v23 A3542 2Pout·2Bout 4   0.50   0.98   0.87 yes 4qcn A3366 2Pout·2Bout 4   0.50   0.99   0.87 no 3v27 A3407 2Pout·2Bout 3   0.36   0.66   0.87 no 4ji6 A1887 2Pout·2Bout 6   0.97   0.98   0.87 yes 4dr1 A1638 2Pout·2Bout 3   0.55   0.63   0.87 no 4nw0 A3149 2Pout·2Bout 3   0.37   0.67   0.87 no 3d2x B83 2Pout·2Bout 3   0.14   0.35   0.87 no 4gar A3118 2Pout·2Bout 6   0.75   1.00   0.86 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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