MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 639 Mg2+ binding sites with the site type 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 1 of 26 | « 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 1dno A24 3Bout 6   0.96   0.99   0.87 yes 1dno B22 3Bout 6   0.96   1.00   0.97 yes 1dnt A21 3Bout 6   0.96   1.00   0.78 yes 1hr2 B21 3Bout 6   0.86   0.96   1.00 yes 1hr2 A26 3Bout 6   0.86   0.96   1.00 yes 1hr2 B23 3Bout 6   0.86   0.96   1.00 yes 1hr2 A24 3Bout 6   0.86   0.96   1.00 yes 1j1u B1502 3Bout 6   0.79   0.89   0.98 yes 1jzv C300 3Bout 6   0.79   0.84   0.82 yes 1k9m A8100 3Bout 5   0.41   0.44   0.77 no 1kc8 A8100 3Bout 5   0.61   0.45   0.69 no 1n8r A8063 3Bout 6   0.84   0.80   0.78 yes 1nuj G421 3Bout 6   0.70   0.92   0.80 yes 1nuj C426 3Bout 6   0.63   0.89   0.75 yes 1nuj G420 3Bout 6   0.76   0.96   0.83 yes 1nuj E423 3Bout 6   0.73   0.93   0.79 yes 1nuj A418 3Bout 6   0.69   0.94   0.80 yes 1nuj E424 3Bout 6   0.70   0.89   0.65 yes 1nuj C425 3Bout 6   0.73   0.81   0.60 yes 1nuj A417 3Bout 6   0.80   0.95   0.82 yes 1nuv C418 3Bout 5   0.36   0.68   0.94 no 1nuv A410 3Bout 6   0.92   0.85   0.82 yes 1nuv A411 3Bout 6   0.78   0.88   0.96 yes 1nuv G413 3Bout 6   0.98   0.81   0.70 yes 1nuv C419 3Bout 4   0.36   0.65   0.41 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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