MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qal:A2136, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout Schematic drawing for 3Pout·Rout List of all 101 Mg2+ binding sites with the site type 3Pout·Rout 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 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vs6 B2955 3Pout·Rout 6   0.97   1.00   1.00 yes 1vs6 B2908 3Pout·Rout 6   0.97   1.00   1.00 yes 1vs6 B3004 3Pout·Rout 6   0.97   1.00   0.50 no 1vt2 A3023 3Pout·Rout 4   0.67   0.99   0.66 yes 2aw4 B2921 3Pout·Rout 6   0.97   0.99   1.00 yes 2aw4 B3004 3Pout·Rout 6   0.97   0.99   0.50 no 2awb B2967 3Pout·Rout 6   0.97   1.00   0.99 yes 2i2t B2955 3Pout·Rout 6   0.97   0.99   1.00 yes 2i2v B2936 3Pout·Rout 6   0.97   0.99   1.00 yes 2qal A2136 3Pout·Rout 6   0.97   1.00   1.00 yes 2qbc B3375 3Pout·Rout 6   0.97   0.99   1.00 yes 2qbh A1589 3Pout·Rout 6   0.97   1.00   1.00 yes 2qbk B2968 3Pout·Rout 6   0.97   1.00   1.00 yes 2qbk B2936 3Pout·Rout 6   0.97   0.99   1.00 yes 2qov B2968 3Pout·Rout 6   0.97   1.00   1.00 yes 2qoz B3004 3Pout·Rout 6   0.97   1.00   1.00 yes 2xzm 019 3Pout·Rout 6   0.11   0.99   1.00 no 2xzm 087 3Pout·Rout 6   0.13   1.00   1.00 no 2z4k A1566 3Pout·Rout 6   0.97   0.99   1.00 yes 2z4l B2956 3Pout·Rout 6   0.97   1.00   1.00 yes 3ccq 08056 3Pout·Rout 6   0.39   0.78   0.80 no 3df1 A2136 3Pout·Rout 6   0.97   1.00   0.49 no 3g4s 08030 3Pout·Rout 4   0.10   0.43   0.93 no 3i1m A1574 3Pout·Rout 6   0.75   0.99   0.65 yes 3i1n A2918 3Pout·Rout 6   0.74   0.98   0.37 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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