MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbg:B2930, See in JSmolClick on the image to toggle views Site type: Pout·4Bout Schematic drawing for Pout·4Bout List of all 174 Mg2+ binding sites with the site type Pout·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 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1hr2 B17 Pout·4Bout 6   0.86   0.96   0.99 yes 1vq7 08100 Pout·4Bout 5   0.41   0.66   0.93 no 1vs5 A1549 Pout·4Bout 6   0.97   1.00   1.00 yes 1vs8 B2923 Pout·4Bout 6   0.97   0.99   1.00 yes 1vt2 A2943 Pout·4Bout 6   0.75   0.98   0.87 yes 1vt2 A2980 Pout·4Bout 6   0.74   0.99   0.65 yes 1yj9 08100 Pout·4Bout 5   0.27   0.50   0.83 no 2aw4 B2983 Pout·4Bout 6   0.97   0.99   1.00 yes 2awb B2930 Pout·4Bout 6   0.97   0.99   1.00 yes 2awb B2923 Pout·4Bout 6   0.97   0.99   0.99 yes 2i2p A1562 Pout·4Bout 6   0.97   1.00   1.00 yes 2i2v B2923 Pout·4Bout 6   0.97   1.00   1.00 yes 2i2v B2930 Pout·4Bout 6   0.97   1.00   1.00 yes 2qal A2129 Pout·4Bout 6   0.97   0.99   1.00 yes 2qal A2115 Pout·4Bout 6   0.97   0.99   1.00 yes 2qam B3103 Pout·4Bout 6   0.97   0.99   1.00 yes 2qan A2141 Pout·4Bout 6   0.97   0.99   1.00 yes 2qao B3110 Pout·4Bout 6   0.97   1.00   0.98 yes 2qba B3103 Pout·4Bout 6   0.97   0.99   1.00 yes 2qbc B3110 Pout·4Bout 6   0.97   1.00   1.00 yes 2qbe B3103 Pout·4Bout 6   0.97   1.00   1.00 yes 2qbg B2930 Pout·4Bout 6   0.97   1.00   1.00 yes 2qbg B2923 Pout·4Bout 6   0.97   1.00   1.00 yes 2qbi B2922 Pout·4Bout 6   0.97   0.99   1.00 yes 2qbj A1562 Pout·4Bout 6   0.97   0.99   1.00 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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