MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2avy:A1578, See in JSmolClick on the image to toggle views Site type: Pout·Rout Schematic drawing for Pout·Rout List of all 142 Mg2+ binding sites with the site type Pout·Rout 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 4 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dhc A3168 Pout·Rout 1   0.02  0   0.88 no 4dhc A3580 Pout·Rout 2   0.24   0.41   0.68 no 4dha A3579 Pout·Rout 5   0.64   0.78   0.85 yes 4dha A3782 Pout·Rout 4   0.48   0.97   0.68 no 4dh9 A1959 Pout·Rout 4   0.49   0.97   0.78 no 4bpp A5007 Pout·Rout 6   0.74   0.99   1.00 yes 4bpo A5007 Pout·Rout 6   0.74   0.99   1.00 yes 4bpo A5052 Pout·Rout 6   0.75   1.00   1.00 yes 4bpn A5007 Pout·Rout 6   0.74   0.99   1.00 yes 4bpn A5052 Pout·Rout 6   0.75   0.99   1.00 yes 4bpe A5007 Pout·Rout 6   0.74   0.99   1.00 yes 4a1a 08 Pout·Rout 6   0.75   0.99   1.00 yes 3v2f A3247 Pout·Rout 3   0.37   0.40   0.76 no 3v2f A3477 Pout·Rout 3   0.35   0.65   0.56 no 3v2f A3465 Pout·Rout 3   0.35   0.62   0.79 no 3v2f A3590 Pout·Rout 2   0.25   0.37   0.87 no 3v2f A3344 Pout·Rout 1   0.12  0   0.92 no 3v2d A3569 Pout·Rout 2   0.22   0.32   0.72 no 3v2d A3695 Pout·Rout 4   0.48   0.63   0.72 no 3v2d A3652 Pout·Rout 4   0.47   0.98   0.51 no 3v2d A3609 Pout·Rout 2   0.22   0.53   0.62 no 3v2d A3577 Pout·Rout 3   0.37   0.61   0.58 no 3v2d A3427 Pout·Rout 3   0.35   0.67   0.58 no 3v2c A1749 Pout·Rout 3   0.37   0.44   0.93 no 3v2c I201 Pout·Rout 2   0.25   0.39   0.94 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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