MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 472 Mg2+ binding sites with the site type Pout·3Bout 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 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 3v23 A3374 Pout·3Bout 5   0.59   0.80   0.72 yes 3v23 A3367 Pout·3Bout 6   0.76   0.97   0.92 yes 3v2f A3367 Pout·3Bout 5   0.62   0.80   0.86 yes 4nvx A3360 Pout·3Bout 3   0.38   0.39   0.63 no 3v27 A3355 Pout·3Bout 6   0.75   0.96   0.78 yes 4nvx A3351 Pout·3Bout 3   0.38   0.66   0.58 no 4nw1 A3345 Pout·3Bout 3   0.39   0.66   0.91 no 3v2f A3345 Pout·3Bout 5   0.60   0.77   0.84 yes 3v23 A3331 Pout·3Bout 5   0.61   0.78   0.95 yes 4nvv A3329 Pout·3Bout 5   0.64   0.80   0.49 no 4nvz A3324 Pout·3Bout 5   0.64   0.80   0.50 yes 3v2f A3320 Pout·3Bout 3   0.36   0.65   0.82 no 2qba B3309 Pout·3Bout 6   0.97   1.00   1.00 yes 2qao B3308 Pout·3Bout 6   0.97   0.99   1.00 yes 3df4 B3308 Pout·3Bout 6   0.97   1.00   1.00 yes 3v23 A3307 Pout·3Bout 6   0.78   0.99   0.66 yes 4nw1 A3301 Pout·3Bout 3   0.37   0.39   0.81 no 4qcp A3264 Pout·3Bout 5   0.63   0.80   1.00 yes 4qcq A3215 Pout·3Bout 2   0.25   0.28   0.89 no 4qcu A3169 Pout·3Bout 2   0.25   0.28   0.87 no 4qcy A3159 Pout·3Bout 5   0.63   0.79   0.73 yes 4nvu A3145 Pout·3Bout 4   0.51   0.98   0.92 yes 4qcs A3145 Pout·3Bout 4   0.50   0.99   0.82 yes 4qcq A3143 Pout·3Bout 5   0.62   0.80   0.97 yes 4qcu A3139 Pout·3Bout 5   0.63   0.80   0.75 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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