MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2930, See in JSmolClick on the image to toggle views Site type: Oph Schematic drawing for Oph List of all 12521 Mg2+ binding sites with the site type Oph 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 501 | « 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 1b23 R77 Oph 1   0.56  0   0.70 no 1cx0 B408 Oph 1   0.04  0   0.97 no 1cx0 B411 Oph 1   0.02  0   0.94 no 1cx0 B412 Oph 1   0.03  0   0.85 no 1evv A903 Oph 6   0.81   0.91   0.81 yes 1evv A907 Oph 2   0.27   0.55   0.16 no 1evv A909 Oph 3   0.41   0.69   0.29 no 1evv A906 Oph 1   0.39  0   0.86 no 1evv A910 Oph 1   0.32  0   0.39 no 1f27 A37 Oph 6   0.94   0.88   0.35 no 1feu F325 Oph 1   0.14  0   0.90 no 1fjg A1611 Oph 1   0.12  0   0.75 no 1fjg A1561 Oph 1   0.06  0   0.60 no 1fjg A1548 Oph 1   0.23  0   0.52 no 1fjg A1587 Oph 1   0.14  0   0.49 no 1fjg A71 Oph 1   0.14  0   0.74 no 1fjg A1598 Oph 1   0.04  0   0.56 no 1fjg A1601 Oph 1   0.24  0   0.51 no 1fjg A1563 Oph 1   0.17  0   0.74 no 1fjg A1560 Oph 1   0.13  0   0.60 no 1fjg A1558 Oph 1   0.06  0   0.98 no 1fjg A1568 Oph 1   0.05  0   0.57 no 1fjg A1554 Oph 1   0.09  0   0.86 no 1fjg A1569 Oph 1   0.14  0   0.67 no 1fjg A86 Oph 1   0.06  0   0.71 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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