MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2u:A1552, See in JSmolClick on the image to toggle views Site type: 5Bout Schematic drawing for 5Bout List of all 80 Mg2+ binding sites with the site type 5Bout 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1m1k A8100 5Bout 5   0.25   0.45   0.79 no 1vs6 B2906 5Bout 6   0.97   1.00   1.00 yes 1vs7 A1563 5Bout 6   0.97   0.99   1.00 yes 1vt2 A2972 5Bout 6   0.75   0.99   0.93 yes 1w2b 38038 5Bout 6   0.47   0.75   0.75 no 1yj9 08038 5Bout 5   0.94   0.58   0.87 no 2aw4 B2906 5Bout 6   0.97   0.99   1.00 yes 2aw7 A1562 5Bout 6   0.97   0.99   1.00 yes 2i2u A1552 5Bout 6   0.97   1.00   1.00 yes 2qao B3001 5Bout 6   0.97   1.00   1.00 yes 2qbg B2905 5Bout 6   0.97   1.00   1.00 yes 2qbj A1557 5Bout 6   0.97   1.00   1.00 yes 2qoz B2906 5Bout 6   0.97   0.99   1.00 yes 2xzm 061 5Bout 6   0.13   0.99   1.00 no 2z4m A1558 5Bout 6   0.97   0.99   1.00 yes 3df4 B3001 5Bout 6   0.97   0.99   1.00 yes 3i1t A2972 5Bout 6   0.75   1.00   1.00 yes 3i22 A2971 5Bout 6   0.74   0.99   1.00 yes 3ivk M122 5Bout 6   0.75   0.99   1.00 yes 3ivk C134 5Bout 6   0.75   0.99   1.00 yes 3ivk M134 5Bout 6   0.75   1.00   1.00 yes 3ofc A2967 5Bout 6   0.76   0.98   0.67 yes 3r8s A2995 5Bout 6   0.76   0.99   0.99 yes 3v23 A3490 5Bout 6   0.74   0.96   0.59 yes 3v25 A3408 5Bout 4   0.49   0.96   0.81 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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