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 4dv1 4DV1 (3.85Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u20g, bound with streptomycin List of all 28 Mg2+ binding sites in the PDB structure 4dv1 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" Page 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dv1 A1767 3Pout·Bout A2106, A2107, A2108, A2109, A2110 C:A1103, C:A1100, A:A1101 C:A1100 4dv1 A1793 3Pout·Rout·Bout A2120, A2121, A2122, A2123, A2124, A2125 C:A150, A:A151, G:A168 G:A167 G:A168 4dv1 A1821 3Pout·2Bout A2238, A2239, A2240, A2241, A2242, A2243 C:A868, G:A869, C:A857 G:A858, G:A869 4dv1 A1820 3Pout·2Bout A2232, A2233, A2234, A2235, A2236, A2237 U:A757, U:A580, G:A758 G:A581, G:A758 4dv1 A1607 4Pout A1912, A1913, A1914, A1915 U:A751, U:A652, G:A752, C:A651 4dv1 A1812 4Pout·Bout A2217, A2218, A2219, A2220, A2221 A:A509, A:A510, G:A506, C:A507 A:A510 4dv1 A1811 4Pout·Rout·Bout A2212, A2213, A2214, A2215, A2216 U:A114, C:A307, G:A115, C:A47 G:A306 G:A31 4dv1 A1627 5Pout·Rout·Bout A1955, A1956, A1957, A1958 A:A563, G:A557, G:A558, U:A560, C:A562 A:A559 G:A566

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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