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 9 of 48 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2vqf Z46 Oph·Or 2   0.13   0.14   0.66 no 3v2f A3075 Oph·Or 2   0.04   0.14   0.98 no 1n32 A1558 Oph·Or 2   0.14   0.14   0.55 no 4cr1 A2693 Oph·Or 2   0.38   0.14   0.61 no 4dh9 A1602 Oph·Or 2   0.06   0.14   0.91 no 1vvn A1611 Oph·Or 2   0.18   0.14   0.47 no 3i8h A1597 Oph·Or 2   0.07   0.14   0.23 no 3d5d A3084 Oph·Or 2   0.06   0.14   0.52 no 3i9d A1873 Oph·Or 2   0.23   0.14   0.69 no 4nvv A3134 Oph·Or 2   0.07   0.15   0.76 no 2x9r Z30 Oph·Or 2   0.22   0.15   0.26 no 3i9d A1909 Oph·Or 2   0.10   0.15   0.69 no 4btd A4042 Oph·Or 2   0.10   0.15   0.65 no 3v6u A1604 Oph·Or 2   0.28   0.15   0.96 no 3oh7 A3032 Oph·Or 2   0.06   0.15   0.77 no 4nvv A3567 Oph·Or 3   0.17   0.15   0.91 no 4qcy A3050 Oph·Or 2   0.23   0.15   0.66 no 2uuc Z1149 Oph·Or 2   0.33   0.15   0.54 no 3i8g A2212 Oph·Or 2   0.05   0.15   0.55 no 2uuc Z1086 Oph·Or 2   0.14   0.15   0.62 no 3i9b A1665 Oph·Or 2   0.25   0.15   0.97 no 2xg1 Z28 Oph·Or 2   0.17   0.15   0.64 no 2v48 G2209 Oph·Or 2   0.08   0.15   0.05 no 4qcm A1695 Oph·Or 2   0.08   0.15   0.98 no 3pyo A157 Oph·Or 2   0.05   0.15   0.76 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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