MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3509, See in JSmolClick on the image to toggle views Site type: fac-3Oph·Or Schematic drawing for fac-3Oph·Or List of all 34 Mg2+ binding sites with the site type fac-3Oph·Or 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvv A1622 fac-3Oph·Or 4   0.33   0.44   0.12 no 1xmo A1583 fac-3Oph·Or 4   0.45   0.54   0.56 no 2f4v A1571 fac-3Oph·Or 4   0.81   0.59   0.38 no 2qov B2994 fac-3Oph·Or 6   0.72   0.74   0.69 yes 2qoz B2994 fac-3Oph·Or 6   0.65   0.68   0.75 yes 2vhm Z4082 fac-3Oph·Or 6   0.23   0.71   0.67 no 3bo2 B1 fac-3Oph·Or 5   0.53   0.48   0.95 no 3ccm 08001 fac-3Oph·Or 6   0.38   0.73   0.25 no 3cpw 08001 fac-3Oph·Or 6   0.39   0.65   0.60 no 3df2 B3509 fac-3Oph·Or 6   0.63   0.82   0.72 yes 3f1f A5462 fac-3Oph·Or 4   0.32   0.78   0.62 no 3f1f A5907 fac-3Oph·Or 4   0.15   0.26   0.89 no 3huz A2989 fac-3Oph·Or 4   0.19   0.69   0.36 no 3i8h A1607 fac-3Oph·Or 4   0.46   0.38   0.44 no 3knk A2950 fac-3Oph·Or 4   0.46   0.40   0.27 no 3ohd A1573 fac-3Oph·Or 4   0.14   0.31   0.94 no 3t1h A1744 fac-3Oph·Or 4   0.22   0.21   0.17 no 3u5b 22063 fac-3Oph·Or 4   0.12   0.54   1.00 no 3u5d 14291 fac-3Oph·Or 4   0.19   0.42   0.62 no 3uzi A1617 fac-3Oph·Or 4   0.11   0.26   0.94 no 3v23 A3569 fac-3Oph·Or 5   0.29   0.55   0.75 no 3v29 A3090 fac-3Oph·Or 4   0.11   0.42   0.91 no 4dhb A1731 fac-3Oph·Or 5   0.21   0.31   0.93 no 4dr3 A1655 fac-3Oph·Or 5   0.25   0.40   0.72 no 4dv1 A1642 fac-3Oph·Or 5   0.32   0.52   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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