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 10 of 24 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v27 A3163 Ob·Nb 2   0.11   0.18   0.79 no 3v26 A1697 Ob·Nb 4   0.28   0.41   0.97 no 3v26 A1645 Ob·Nb 2   0.03   0.13   0.95 no 3v25 A3284 Ob·Nb 6   0.59   0.79   0.93 yes 3v24 A1649 Ob·Nb 5   0.43   0.50   0.95 no 3v23 A3114 Ob·Nb 2   0.09   0.17   0.95 no 3v22 A1697 Ob·Nb 4   0.29   0.50   0.88 no 3uz7 C124 Ob·Nb 2   0.03   0.23   0.97 no 3uz7 A2003 Ob·Nb 2   0.04   0.14   0.92 no 3u5h 54277 Ob·Nb 2   0.05   0.14   0.72 no 3u5h 54286 Ob·Nb 2   0.15   0.76   1.00 no 3u5h 54561 Ob·Nb 2   0.09   0.37   0.58 no 3u5h 54460 Ob·Nb 2   0.07   0.21   0.64 no 3u5h 54221 Ob·Nb 2   0.06   0.40   0.69 no 3u5h 54191 Ob·Nb 2   0.03   0.14   0.45 no 3u5d 14224 Ob·Nb 2   0.03   0.41   0.69 no 3u5d 14179 Ob·Nb 2   0.04   0.33   0.84 no 3u5d 14236 Ob·Nb 2   0.23   0.15   0.90 no 3u5d 13976 Ob·Nb 2   0.15   0.52   0.97 no 3u5d 13972 Ob·Nb 2   0.03   0.29   0.88 no 3u5d 14603 Ob·Nb 2   0.07   0.24   0.36 no 3u5d 13884 Ob·Nb 2   0.03   0.20   0.76 no 3t1y A1721 Ob·Nb 2   0.05   0.12   0.46 no 3t1y A1700 Ob·Nb 2   0.06   0.11   0.25 no 3t1y A1696 Ob·Nb 2   0.09   0.17   0.30 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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