MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2982, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·3Bout Schematic drawing for 2Pout·Rout·3Bout List of all 57 Mg2+ binding sites with the site type 2Pout·Rout·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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1feu B311 2Pout·Rout·3Bout 5   0.93   0.84   0.77 yes 1m1k A8108 2Pout·Rout·3Bout 5   0.56   0.46   0.61 no 1n8r A8108 2Pout·Rout·3Bout 5   0.48   0.54   0.68 no 1vs6 B2956 2Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 1vs6 B2982 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 1yjw 78071 2Pout·Rout·3Bout 6   0.49   0.49   0.74 no 2aw4 B2982 2Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 2i2t B2956 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qam B3450 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qba B3450 2Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 2qbe B3302 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qbk B2959 2Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 2qoz B2956 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qp1 B2959 2Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2vhn Z4106 2Pout·Rout·3Bout 5   0.28   0.79   0.37 no 2xzm 041 2Pout·Rout·3Bout 6   0.13   1.00   1.00 no 3cd6 08088 2Pout·Rout·3Bout 5   0.16   0.68   0.97 no 3cxc 08108 2Pout·Rout·3Bout 5   0.44   0.65   0.73 no 3df2 B3450 2Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 3i1n A2920 2Pout·Rout·3Bout 6   0.76   0.98   0.71 yes 3i1r A2985 2Pout·Rout·3Bout 6   0.75   0.98   1.00 yes 3i22 A2905 2Pout·Rout·3Bout 6   0.75   1.00   1.00 yes 3i22 A2977 2Pout·Rout·3Bout 6   0.75   1.00   1.00 yes 3oar A1574 2Pout·Rout·3Bout 5   0.82   0.80   0.80 yes 3oat A2919 2Pout·Rout·3Bout 6   0.76   0.99   0.35 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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