MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·Or 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 1 of 48 | « 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 4dv7 A1682 Oph·Or 2   0.04   0.35   0.88 no 2j00 Z170 Oph·Or 2   0.13   0.10   0.49 no 2xfz Z273 Oph·Or 2   0.13   0.32   0.58 no 2xfz Z277 Oph·Or 2   0.23   0.46   0.45 no 4byd A2613 Oph·Or 2   0.28   0.30   0.92 no 3ohj A2989 Oph·Or 2   0.08   0.13   0.53 no 3kni A3112 Oph·Or 2   0.21   0.05   0.75 no 4kvb A1644 Oph·Or 3   0.32   0.40   0.67 no 3v6u A1703 Oph·Or 2   0.31   0.18   0.01 no 4kfh A1707 Oph·Or 2   0.03   0.18   0.76 no 3ow2 08025 Oph·Or 2   0.05   0.58   0.59 no 4dh9 A1602 Oph·Or 2   0.06   0.14   0.91 no 4qln A204 Oph·Or 3   0.31   0.34   0.89 no 4dha A3002 Oph·Or 2   0.04   0.57   0.96 no 3oi5 A2911 Oph·Or 2   0.09   0.26   0.65 no 3kiu a1534 Oph·Or 2   0.37   0.13   0.38 no 3kir A2901 Oph·Or 2   0.06   0.36   0.57 no 1vxs A1613 Oph·Or 2   0.15   0.12   0.33 no 1l8v B314 Oph·Or 2   0.10   0.42   0.88 no 2x9r Z20 Oph·Or 3   0.44   0.57   0.62 no 1n32 A1558 Oph·Or 2   0.14   0.14   0.55 no 1i96 A1528 Oph·Or 2   0.09   0.44   0.67 no 1i95 A1528 Oph·Or 2   0.08   0.51   0.63 no 4nya B104 Oph·Or 2   0.22   0.47   0.66 no 3knk A2983 Oph·Or 2   0.27   0.11   0.25 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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