MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2v48:G2217, See in JSmolClick on the image to toggle views Site type: Oph·Ob·Nb Schematic drawing for Oph·Ob·Nb List of all 149 Mg2+ binding sites with the site type Oph·Ob·Nb 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2vhn Z4037 Oph·Ob·Nb 6   0.19   0.87   0.79 no 3pyr A3004 Oph·Ob·Nb 3   0.05   0.84   0.83 no 3i9b A1898 Oph·Ob·Nb 3   0.35   0.83   0.83 no 4dr6 A1912 Oph·Ob·Nb 3   0.10   0.82   0.91 no 4dv4 A1862 Oph·Ob·Nb 3   0.05   0.82   0.86 no 4dv3 A1705 Oph·Ob·Nb 4   0.08   0.81   0.95 no 4b3r A2699 Oph·Ob·Nb 3   0.09   0.79   0.65 no 1vvo A3217 Oph·Ob·Nb 3   0.07   0.78   0.80 no 2wdm Z49 Oph·Ob·Nb 3   0.04   0.78   0.66 no 1vq9 08094 Oph·Ob·Nb 4   0.11   0.78   0.67 no 4l6j A4771 Oph·Ob·Nb 3   0.07   0.78   0.41 no 2z75 B308 Oph·Ob·Nb 5   0.10   0.78   0.75 no 1vqm 08094 Oph·Ob·Nb 4   0.25   0.76   0.56 no 2j02 Z54 Oph·Ob·Nb 3   0.05   0.76   0.85 no 4l6j A4493 Oph·Ob·Nb 3   0.14   0.75   0.84 no 1vvs A3213 Oph·Ob·Nb 3   0.05   0.75   0.49 no 3f1f A5973 Oph·Ob·Nb 3   0.06   0.74   0.89 no 4l6j A4043 Oph·Ob·Nb 3   0.07   0.73   0.59 no 1vqk 08094 Oph·Ob·Nb 4   0.16   0.73   0.66 no 3umy B2203 Oph·Ob·Nb 5   0.12   0.73   0.60 no 4kfh A2248 Oph·Ob·Nb 3   0.10   0.72   0.98 no 2vho Z4050 Oph·Ob·Nb 5   0.18   0.71   0.57 no 1vqn 08094 Oph·Ob·Nb 4   0.20   0.70   0.67 no 4duz A1767 Oph·Ob·Nb 3   0.06   0.69   0.89 no 2v48 G2217 Oph·Ob·Nb 4   0.56   0.69   0.76 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/)
For any help please contact <dust@iwonka.med.virginia.edu>