MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3owi 3OWI (2.85Å) -- RNA : Crystal structure of the glycine riboswitch bound to glycine List of all 30 Mg2+ binding sites in the PDB structure 3owi 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 #", "Site type" or "Mg2+ ID" Page 1 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3owi A115 Nb 6   0.74   0.98   0.58 yes 3owi B112 Nb 6   0.71   0.93   0.56 yes 3owi A127 2Ob 2   0.08   0.20   0.65 no 3owi B120 Oph 1   0.13  0   0.63 no 3owi B119 Oph 1   0.05  0   0.65 no 3owi A118 Oph·Pout 6   0.80   0.93   0.65 yes 3owi B117 Oph·Pout 6   0.69   0.91   0.69 yes 3owi A116 Oph·Pout 6   0.82   0.91   0.71 yes 3owi A111 Oph·3Pout 6   0.72   0.91   0.56 yes 3owi A123 Oph·Nb 2   0.04   0.35   0.72 no 3owi A101 cis-2Oph 6   0.90   0.88   0.78 yes 3owi A105 cis-2Oph 6   0.73   0.93   0.69 yes 3owi A125 cis-2Oph 2   0.08   0.31   0.63 no 3owi B113 cis-2Oph 6   0.72   0.93   0.60 yes 3owi B122 cis-2Oph 2   0.17   0.19   0.56 no 3owi B133 cis-2Oph 2   0.10   0.25   0.97 no 3owi A103 trans-2Oph 6   0.58   0.93   0.72 yes 3owi B114 cis-2Oph·Or 6   0.78   0.90   0.60 yes 3owi A102 cis-2Oph·Or 6   0.79   0.82   0.64 yes 3owi B121 mer-3Oph 3   0.27   0.43   0.61 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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