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 2 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 2wdk Z235 Oph·Ob·Nb 3   0.13   0.25   0.80 no 3i8g A1989 Oph·Ob·Nb 3   0.16   0.26   0.62 no 4nvu A3035 Oph·Ob·Nb 3   0.16   0.26   0.82 no 3tvf A2085 Oph·Ob·Nb 3   0.07   0.27   0.74 no 4qd1 A3253 Oph·Ob·Nb 3   0.35   0.28   0.75 no 3u5d 14005 Oph·Ob·Nb 3   0.07   0.29   1.00 no 4too A3145 Oph·Ob·Nb 3   0.19   0.29   0.73 no 4e8r A415 Oph·Ob·Nb 4   0.20   0.30   0.86 no 3huw A1640 Oph·Ob·Nb 3   0.11   0.30   0.50 no 1vvy A3043 Oph·Ob·Nb 3   0.36   0.30   0.49 no 4eja A7124 Oph·Ob·Nb 3   0.11   0.30   0.54 no 4qcv A3570 Oph·Ob·Nb 4   0.17   0.30   0.84 no 3i8h A1988 Oph·Ob·Nb 3   0.12   0.31   0.92 no 4ji0 A1801 Oph·Ob·Nb 3   0.14   0.32   1.00 no 3oi3 B189 Oph·Ob·Nb 3   0.23   0.32   0.86 no 3i9d A1608 Oph·Ob·Nb 3   0.13   0.32   0.55 no 4kja A1627 Oph·Ob·Nb 4   0.15   0.32   0.76 no 2wdg Z217 Oph·Ob·Nb 3   0.53   0.33   0.87 no 4qcr A3632 Oph·Ob·Nb 4   0.18   0.35   0.78 no 2j00 Z217 Oph·Ob·Nb 3   0.32   0.35   0.92 no 3d5a A1639 Oph·Ob·Nb 3   0.15   0.36   0.24 no 4dr6 A1797 Oph·Ob·Nb 3   0.06   0.36   0.91 no 1xnq A467 Oph·Ob·Nb 3   0.13   0.37   0.69 no 4ej9 A7103 Oph·Ob·Nb 3   0.18   0.38   0.42 no 4nvu A3036 Oph·Ob·Nb 3   0.09   0.39   0.98 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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