MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qao:B3320, See in JSmolClick on the image to toggle views Site type: 3Pout·4Bout Schematic drawing for 3Pout·4Bout List of all 28 Mg2+ binding sites with the site type 3Pout·4Bout 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vs8 B2938 3Pout·4Bout 6   0.97   0.99   1.00 yes 2qam B3110 3Pout·4Bout 6   0.97   1.00   1.00 yes 2qao B3320 3Pout·4Bout 6   0.97   1.00   1.00 yes 2qbe B3110 3Pout·4Bout 6   0.97   1.00   1.00 yes 2qbi B2983 3Pout·4Bout 6   0.97   0.99   1.00 yes 2qbi B2923 3Pout·4Bout 6   0.97   1.00   1.00 yes 2qov B2956 3Pout·4Bout 6   0.97   0.99   1.00 yes 2qov B2983 3Pout·4Bout 6   0.97   1.00   1.00 yes 2qoz B2983 3Pout·4Bout 6   0.97   0.99   1.00 yes 2qoz B2923 3Pout·4Bout 6   0.97   0.99   1.00 yes 2vhn Z4027 3Pout·4Bout 4   0.17   0.61   0.78 no 2z4l B2984 3Pout·4Bout 6   0.97   0.99   1.00 yes 2z4n B2931 3Pout·4Bout 6   0.97   0.99   1.00 yes 3ofz A2905 3Pout·4Bout 6   0.75   0.99   0.82 yes 3r8s A2905 3Pout·4Bout 6   0.76   0.98  0 no 3r8t A2905 3Pout·4Bout 6   0.75   0.97   1.00 yes 3v23 A3608 3Pout·4Bout 6   0.80   0.96   0.76 yes 3v2d A3402 3Pout·4Bout 6   0.80   0.97   0.81 yes 4a17 0325 3Pout·4Bout 6   0.74   0.99   0.99 yes 4gar A3002 3Pout·4Bout 6   0.75   1.00   0.97 yes 4qcn A3297 3Pout·4Bout 4   0.40   0.76   0.55 no 4tom A3002 3Pout·4Bout 6   0.73   0.98   0.38 no 4tp1 A3072 3Pout·4Bout 6   0.75   0.99   0.78 yes 4tp3 A3080 3Pout·4Bout 4   0.67   0.64   0.95 yes 4tp7 A3081 3Pout·4Bout 4   0.67   0.65   0.97 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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