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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4duz



4DUZ (3.65Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c, bound with streptomycin
List of all 24 Mg2+ binding sites in the PDB structure 4duz in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4duz A1842 3Pout·Rout·Bout A2228, A2229, A2230, A2231, A2232 G:A951, G:A1224, U:A952 C:A1223 A:A977
4duz A1839 3Pout·2Bout A2212, A2213, A2214, A2215, A2216, A2217 G:A581, U:A757, U:A580 G:A758, G:A581
4duz A1840 3Pout·2Bout A2218, A2219, A2220, A2221, A2222 G:A858, C:A868, C:A857 G:A858, G:A869
4duz A1829 4Pout·Bout A2198, A2199, A2200, A2201, A2202, A2203 A:A509, A:A510, G:A506, C:A507 A:A510

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>