MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1hr2:A5, See in JSmolClick on the image to toggle views Site type: Ob·Nb Schematic drawing for Ob·Nb List of all 592 Mg2+ binding sites with the site type 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 6 of 24 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4ji1 A1868 Ob·Nb 2   0.04   0.13   0.81 no 4ji0 A1785 Ob·Nb 2   0.04   0.26   0.98 no 4ji0 A1787 Ob·Nb 2   0.03   0.17   0.86 no 4ji0 A1721 Ob·Nb 2   0.04   0.15   0.90 no 4ji0 A1710 Ob·Nb 3   0.18   0.14   0.64 no 4hub 08095 Ob·Nb 2   0.12   0.28   0.73 no 4gd1 A1660 Ob·Nb 2   0.03   0.14   0.37 no 4g5v A1715 Ob·Nb 2   0.22   0.26   0.90 no 4g5v A1867 Ob·Nb 2   0.07   0.16   0.96 no 4g5v A1645 Ob·Nb 2   0.22   0.19   0.99 no 4g5v A1873 Ob·Nb 2   0.05   0.16   0.89 no 4g5t A1920 Ob·Nb 2   0.27   0.24   0.99 no 4g5t A1623 Ob·Nb 2   0.05   0.12   0.87 no 4g5t A1715 Ob·Nb 2   0.09   0.16   0.97 no 4g5m A1953 Ob·Nb 2   0.04   0.13   1.00 no 4g5k A1636 Ob·Nb 2   0.05   0.11   0.59 no 4g5k A1754 Ob·Nb 2   0.05   0.13   0.81 no 4g5k C137 Ob·Nb 2   0.03   0.27   0.89 no 4fb0 A409 Ob·Nb 3   0.11   0.24   0.60 no 4far A407 Ob·Nb 4   0.18   0.29   0.84 no 4e8p A407 Ob·Nb 2   0.08   0.12   0.58 no 4e8m A406 Ob·Nb 2   0.06   0.20   0.46 no 4dv6 A1767 Ob·Nb 2   0.03   0.22   0.79 no 4dv6 A1746 Ob·Nb 2   0.03   0.14   0.95 no 4dv5 A1753 Ob·Nb 2   0.04   0.15   0.59 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>