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 5 of 24 | « 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 4kj7 A3044 Ob·Nb 3   0.24   0.13   0.65 no 4kj7 A3092 Ob·Nb 2   0.08   0.15   0.67 no 4kj5 A3044 Ob·Nb 4   0.37   0.42   0.56 no 4kj5 A3070 Ob·Nb 5   0.50   0.25   0.77 no 4kj4 A1615 Ob·Nb 4   0.15   0.87   0.91 no 4kj3 B1203 Ob·Nb 3   0.25   0.35   0.69 no 4kj3 A3071 Ob·Nb 4   0.41   0.51   0.93 no 4kj3 A3095 Ob·Nb 4   0.15   0.62   0.30 no 4kix A3089 Ob·Nb 5   0.16   0.78   0.75 no 4kfk A2191 Ob·Nb 2   0.05   0.12   0.70 no 4kfh A2549 Ob·Nb 2   0.03   0.38   0.48 no 4kfh A2717 Ob·Nb 2   0.03   0.20   0.73 no 4kfh A1698 Ob·Nb 2   0.07   0.32   0.57 no 4ji8 A1666 Ob·Nb 2   0.03   0.14   0.84 no 4ji6 A1720 Ob·Nb 2   0.08   0.13   0.81 no 4ji6 A1662 Ob·Nb 2   0.05   0.13   0.86 no 4ji6 A1659 Ob·Nb 2   0.04   0.15   0.97 no 4ji5 A1636 Ob·Nb 6   0.68   0.68   0.70 yes 4ji5 A1673 Ob·Nb 2   0.05   0.16   0.76 no 4ji5 A1635 Ob·Nb 2   0.04   0.13   0.87 no 4ji5 A1730 Ob·Nb 2   0.07   0.10   0.84 no 4ji4 A1706 Ob·Nb 5   0.52   0.74   0.79 yes 4ji2 A1685 Ob·Nb 6   0.65   0.72   0.57 yes 4ji2 A1813 Ob·Nb 2   0.09   0.24   0.93 no 4ji2 A1808 Ob·Nb 2   0.10   0.28   0.79 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>