MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 67 | « 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 4jya A1613 2Ob 2   0.03   0.19   0.57 no 2uuc Z1070 2Ob 2   0.03   0.16   0.86 no 4dv3 A1796 2Ob 2   0.03   0.14   0.81 no 3f1f A5703 2Ob 2   0.03   0.21   0.68 no 4btd A4141 2Ob 2   0.03   0.17   0.81 no 3v26 A1677 2Ob 2   0.03   0.12   0.80 no 3u5f 62239 2Ob 2   0.03   0.32   0.77 no 4qcm A1675 2Ob 2   0.03   0.18   0.78 no 4ji4 A1696 2Ob 2   0.03   0.17   0.78 no 2wdg Z297 2Ob 2   0.03   0.16   0.88 no 3tvf A2382 2Ob 2   0.03   0.18   0.76 no 4nvu A3124 2Ob 2   0.03   0.17   0.96 no 4dv5 A1759 2Ob 2   0.03   0.18   0.83 no 4dv0 A1730 2Ob 2   0.03   0.17   0.66 no 3d5a A1596 2Ob 2   0.03   0.43   0.26 no 4l6j A5166 2Ob 2   0.03   0.16   0.80 no 4dv7 A1748 2Ob 2   0.03   0.11   0.79 no 4tp9 A3174 2Ob 2   0.03   0.16   0.82 no 4dv5 A1760 2Ob 2   0.03   0.14   0.97 no 3ohk A3054 2Ob 2   0.03   0.19   0.83 no 4ji6 A1944 2Ob 2   0.03   0.26   0.78 no 3kix a1656 2Ob 2   0.03   0.45   0.93 no 3f1f A5921 2Ob 2   0.03   0.17   0.49 no 3v29 A3125 2Ob 2   0.03   0.21   1.00 no 4ji2 A1774 2Ob 2   0.03   0.12   0.67 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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