MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 3 of 67 | « 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 3oi1 A159 2Ob 2   0.05   0.17   0.88 no 2j00 Z161 2Ob 2   0.11   0.28   0.24 no 3oi5 A161 2Ob 2   0.04   0.20   0.94 no 3ohk A161 2Ob 2   0.05   0.27   0.98 no 2wdg Z161 2Ob 2   0.20   0.29   0.48 no 2v46 Z161 2Ob 2   0.11   0.25   0.55 no 3ohz A163 2Ob 2   0.07   0.14   0.67 no 3oi1 A163 2Ob 2   0.08   0.42   0.87 no 3oh7 A163 2Ob 2   0.06   0.25   0.99 no 3hux A163 2Ob 2   0.04   0.22   0.49 no 2uua Z164 2Ob 2   0.05   0.24   0.74 no 2wh3 Z166 2Ob 2   0.06   0.16   0.77 no 3ohz A166 2Ob 2   0.03   0.20   0.80 no 3pyo A167 2Ob 2   0.06   0.24   0.59 no 3pyt A168 2Ob 2   0.07   0.21   0.88 no 3huz A168 2Ob 2   0.06   0.25   0.34 no 3oi3 A169 2Ob 2   0.04   0.20   0.75 no 3ms1 A169 2Ob 2   0.06   0.47   0.43 no 2uua Z171 2Ob 2   0.06   0.21   0.96 no 2uua Z172 2Ob 2   0.05   0.18   0.79 no 2wdk Z173 2Ob 2   0.03   0.20   0.76 no 2wh1 Z174 2Ob 2   0.04   0.20   0.50 no 2uxc Z174 2Ob 2   0.05   0.16   0.86 no 2j00 Z179 2Ob 2   0.03   0.19   0.88 no 2x9r Z181 2Ob 2   0.04   0.16   0.65 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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