MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1yhq:08001, See in JSmolClick on the image to toggle views Site type: fac-3Oph Schematic drawing for fac-3Oph List of all 1374 Mg2+ binding sites with the site type fac-3Oph 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 55 | « 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 1ffk 02925 fac-3Oph 6   0.70   0.86   0.94 yes 1fjg A1579 fac-3Oph 3   0.30   0.22   0.50 no 1fjg A1595 fac-3Oph 3   0.30   0.29   0.60 no 1gid A267 fac-3Oph 3   0.31   0.26   0.80 no 1gid B269 fac-3Oph 3   0.27   0.25   0.85 no 1hnz A1594 fac-3Oph 3   0.24   0.38   0.56 no 1hr2 B2 fac-3Oph 6   0.96   0.84   0.97 yes 1hr2 A1 fac-3Oph 6   0.96   0.89   0.89 yes 1i94 A1567 fac-3Oph 3   0.19   0.25   0.90 no 1i96 A1569 fac-3Oph 3   0.18   0.22   0.99 no 1ibl A1587 fac-3Oph 3   0.41   0.37   0.44 no 1ibm A1588 fac-3Oph 3   0.45   0.35   0.48 no 1j1u B1501 fac-3Oph 5   0.52   0.79   0.96 yes 1jj2 08016 fac-3Oph 6   0.87   0.90   0.85 yes 1jj2 08001 fac-3Oph 6   0.92   0.94   0.97 yes 1jj2 08026 fac-3Oph 6   0.93   0.92   0.89 yes 1jj2 08003 fac-3Oph 6   0.83   0.91   0.88 yes 1k73 A8026 fac-3Oph 6   0.71   0.86   0.43 no 1k73 A8006 fac-3Oph 6   0.74   0.77   0.80 yes 1k73 A8001 fac-3Oph 6   0.98   0.67   0.54 yes 1k73 A8003 fac-3Oph 6   0.93   0.86   0.67 yes 1k73 A8016 fac-3Oph 6   0.97   0.84   0.75 yes 1k8a A8016 fac-3Oph 6   0.79   0.84   0.69 yes 1k8a A8003 fac-3Oph 6   0.78   0.82   0.44 no 1k8a A8001 fac-3Oph 6   0.99   0.73   0.87 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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