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 2x9r Z1 Oph·Or 2   0.03   0.33   0.57 no 2wdg Z5 Oph·Or 2   0.47   0.20   0.81 no 2uxc Z13 Oph·Or 2   0.08   0.06   0.90 no 2quw C14 Oph·Or 2   0.08   0.25   0.85 no 2x9r Z20 Oph·Or 3   0.44   0.57   0.62 no 2vqf Z20 Oph·Or 2   0.07   0.54   0.76 no 3kix x22 Oph·Or 3   0.18   0.37   0.49 no 2xg1 Z27 Oph·Or 2   0.17   0.16   0.70 no 2xg1 Z28 Oph·Or 2   0.17   0.15   0.64 no 2x9r Z30 Oph·Or 2   0.22   0.15   0.26 no 2x9r Z36 Oph·Or 2   0.13   0.05   0.37 no 2uua Z45 Oph·Or 2   0.23   0.05   0.71 no 2vqf Z46 Oph·Or 2   0.13   0.14   0.66 no 2vqe Z46 Oph·Or 2   0.16   0.13   0.56 no 2zm5 C81 Oph·Or 2   0.15   0.12   0.70 no 3oi3 A91 Oph·Or 2   0.08   0.27   0.85 no 2vqf Z94 Oph·Or 2   0.25   0.25   0.98 no 2vqe Z94 Oph·Or 2   0.17   0.18   0.67 no 2uua Z99 Oph·Or 2   0.19   0.22   0.57 no 3d5b A100 Oph·Or 2   0.03   0.61  0 no 4qcr 6101 Oph·Or 3   0.19   0.67   0.89 no 3owz A102 Oph·Or 6   0.82   0.80   0.83 yes 4mgn D104 Oph·Or 2   0.17   0.13   0.99 no 4nya B104 Oph·Or 2   0.22   0.47   0.66 no 4tzz E104 Oph·Or 2   0.06   0.21   0.45 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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