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 3 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 1hnw A1547 Oph 1   0.24  0   0.36 no 1hnw A1557 Oph 1   0.07  0   0.76 no 1hnw A1585 Oph 1   0.24  0   0.38 no 1hnw A1609 Oph 1   0.04  0   0.66 no 1hnw A1570 Oph 1   0.06  0   0.68 no 1hnx A86 Oph 1   0.18  0   0.60 no 1hnx A1554 Oph 1   0.06  0   0.67 no 1hnx A1597 Oph 1   0.08  0   0.62 no 1hnx A214 Oph 1   0.03  0   0.73 no 1hnx A1560 Oph 1   0.03  0   0.62 no 1hnx A1610 Oph 1   0.07  0   0.65 no 1hnx A1559 Oph 1   0.16  0   0.50 no 1hnx A1562 Oph 1   0.17  0   0.54 no 1hnx A1600 Oph 1   0.15  0   0.43 no 1hnx A71 Oph 1   0.14  0   0.56 no 1hnx A1556 Oph 1   0.01  0   0.69 no 1hnx A1547 Oph 1   0.22  0   0.43 no 1hnx A1570 Oph 1   0.02  0   0.75 no 1hnx A1586 Oph 1   0.12  0   0.44 no 1hnx A1550 Oph 1   0.02  0   0.65 no 1hnx A1567 Oph 1   0.10  0   0.43 no 1hnx A1553 Oph 1   0.12  0   0.76 no 1hnx A1557 Oph 1   0.07  0   0.67 no 1hnx A1568 Oph 1   0.06  0   0.54 no 1hnz A86 Oph 1   0.04  0   0.60 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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