MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qov:B2933, See in JSmolClick on the image to toggle views Site type: Oph·3Pout Schematic drawing for Oph·3Pout List of all 1171 Mg2+ binding sites with the site type Oph·3Pout 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 8 of 47 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vqk 08032 Oph·3Pout 6   0.67   0.75   0.88 yes 1vqk 08036 Oph·3Pout 6   0.57   0.88   0.94 yes 1vqk 08017 Oph·3Pout 6   0.91   0.68   0.63 yes 1vql 08032 Oph·3Pout 6   0.61   0.82   0.85 yes 1vql 08017 Oph·3Pout 6   0.83   0.85   0.82 yes 1vql 08036 Oph·3Pout 6   0.68   0.92   0.96 yes 1vqm 08036 Oph·3Pout 6   0.53   0.83   0.92 yes 1vqm 08017 Oph·3Pout 6   0.88   0.80   0.84 yes 1vqm 08032 Oph·3Pout 6   0.64   0.82   0.93 yes 1vqn 08036 Oph·3Pout 6   0.63   0.88   0.89 yes 1vqn 08017 Oph·3Pout 6   0.87   0.77   0.89 yes 1vqn 08058 Oph·3Pout 5   0.51   0.87   0.86 yes 1vqn 08032 Oph·3Pout 6   0.63   0.76   0.90 yes 1vqo 08017 Oph·3Pout 6   0.86   0.72   0.75 yes 1vqo 08036 Oph·3Pout 6   0.70   0.86   0.87 yes 1vqp 08017 Oph·3Pout 6   0.82   0.89   0.93 yes 1vqp 08036 Oph·3Pout 6   0.77   0.93   0.94 yes 1vs5 A1550 Oph·3Pout 6   0.88   0.89   0.96 yes 1vs6 B2920 Oph·3Pout 6   0.99   0.96   0.92 yes 1vs6 B2979 Oph·3Pout 6   0.84   0.83   0.96 yes 1vs6 B3003 Oph·3Pout 6   0.91   0.93   0.91 yes 1vs6 B2912 Oph·3Pout 6   0.99   0.97   0.93 yes 1vs6 B2999 Oph·3Pout 6   0.89   0.87   1.00 yes 1vs6 B2933 Oph·3Pout 6   0.87   0.85   0.83 yes 1vs6 B2967 Oph·3Pout 5   0.84   0.83   0.93 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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