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 3v7e D412 Ob·Nb 2   0.34   0.05   0.61 no 4ji5 A1635 Ob·Nb 2   0.04   0.13   0.87 no 3i9d A1669 Ob·Nb 2   0.25   0.08   0.51 no 3d5c A1846 Ob·Nb 2   0.05   0.16   0.22 no 1vvp A1636 Ob·Nb 2   0.40   0.04   0.22 no 4qd1 A3039 Ob·Nb 2   0.05   0.46   0.89 no 3ivk C137 Ob·Nb 2   0.03   0.14   0.99 no 3huw A1567 Ob·Nb 2   0.08   0.17   1.00 no 2uub Z1141 Ob·Nb 2   0.05   0.43   0.64 no 3knj A1572 Ob·Nb 2   0.20   0.11   0.36 no 3oi4 A1584 Ob·Nb 2   0.07   0.11   0.77 no 3i8g A1987 Ob·Nb 2   0.06   0.12   0.98 no 2x9t Z132 Ob·Nb 2   0.05   0.10   0.88 no 3v26 A1645 Ob·Nb 2   0.03   0.13   0.95 no 4dv3 A1648 Ob·Nb 2   0.03   0.17   0.86 no 3u5d 13884 Ob·Nb 2   0.03   0.20   0.76 no 4lfa A1652 Ob·Nb 2   0.05   0.15   0.91 no 4dr5 A1652 Ob·Nb 2   0.06   0.17   0.85 no 3v6u A1661 Ob·Nb 2   0.09   0.14   0.03 no 4tp0 A1655 Ob·Nb 2   0.58   0.39   0.83 no 4ji6 A1659 Ob·Nb 2   0.04   0.15   0.97 no 2uub Z1057 Ob·Nb 2   0.05   0.12   0.75 no 4tp4 A1656 Ob·Nb 2   0.79   0.32   0.91 no 4tou A1657 Ob·Nb 2   0.30   0.28   0.50 no 4g5k A1754 Ob·Nb 2   0.05   0.13   0.81 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>