MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 234 Mg2+ binding sites with the site type 4Pout 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 10 | « 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 1ehz A560 4Pout 6   0.79   1.00   0.93 yes 1ffy T1201 4Pout 6   0.72   0.99   0.99 yes 1qu2 T1201 4Pout 6   0.72   0.99   0.99 yes 1vs5 A1560 4Pout 6   0.97   1.00   1.00 yes 1vs5 A1556 4Pout 6   0.97   1.00   1.00 yes 1vs7 A1557 4Pout 6   0.97   1.00   1.00 yes 1vs7 A1549 4Pout 6   0.97   0.99   1.00 yes 1vs7 A1551 4Pout 6   0.97   1.00   1.00 yes 1vs8 B2961 4Pout 6   0.97   0.99   0.50 no 1yls D247 4Pout 6   0.81   0.99   0.99 yes 2avy A1559 4Pout 6   0.97   0.99   1.00 yes 2aw7 A1550 4Pout 6   0.97   0.99   1.00 yes 2aw7 A1556 4Pout 6   0.97   0.99   1.00 yes 2aw7 A1548 4Pout 6   0.97   0.99   1.00 yes 2awb B2962 4Pout 6   0.97   0.99   0.50 no 2i2t B3022 4Pout 6   0.97   1.00   1.00 yes 2i2t B2908 4Pout 6   0.97   1.00   1.00 yes 2i2t B3004 4Pout 6   0.97   1.00   1.00 yes 2i2v B2967 4Pout 6   0.97   0.99   1.00 yes 2i2v B3023 4Pout 6   0.97   1.00   1.00 yes 2otl 08072 4Pout 5   0.71   0.74   0.92 yes 2qal A2096 4Pout 6   0.97   1.00   1.00 yes 2qam B3382 4Pout 6   0.97   1.00   1.00 yes 2qan A2029 4Pout 6   0.97   1.00   1.00 yes 2qan A2077 4Pout 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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