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 4dv3 4DV3 (3.55Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, c912a, bound with streptomycin List of all 28 Mg2+ binding sites in the PDB structure 4dv3 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 1 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 4dv3 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376 4dv3 A1627 Ob G:A305(O6) A1953, A1954, A1955 C:A291 U:A304, G:A293 4dv3 A1668 Nb G:A362(N7) A2024, A2025, A2026, A2027 G:A361, G:A362 4dv3 A1614 Oph G:A21(OP1) A1930, A1931, A1932 G:A567, A:A573 4dv3 A1631 Oph·Pout G:A588(OP2) A1961, A1962, A1963 G:A644 G:A644 4dv3 A1619 Oph·Pout A:A768(OP2) A1937, A1938, A1939, A1940 C:A805 A:A768 4dv3 A1652 Oph·Pout C:A352(OP2) A2000, A2001, A2002, A2003, A2004 G:A354 G:A331, C:A352 A:A59, G:A354 4dv3 A1651 Oph·2Pout G:A903(OP1) A1996, A1997, A1998, A1999 U:A891, C:A904 G:A890 G:A906 4dv3 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117 4dv3 A1638 Bout A1973, A1974, A1975, A1976 G:A587 4dv3 A1757 2Bout A2079, A2080, A2081, A2082 G:A595, G:A593 4dv3 A1825 2Bout A2149, A2150, A2151, A2152 G:A474, G:A475 4dv3 A1607 Pout·Bout A1912, A1913, A1914, A1915 U:A751 G:A752 4dv3 A1851 Pout·Rout·Bout A2229, A2230, A2231, A2232, A2233, A2234 G:A1224 C:A1223 A:A977 4dv3 A1856 Pout·2Bout A2253, A2254, A2255, A2256, A2257 G:A391 G:A392, G:A391 4dv3 A1821 Pout·2Bout A2129, A2130, A2131, A2132 G:A1185 G:A1186, G:A1185 4dv3 A1827 Pout·3Bout A2156, A2157, A2158, A2159, A2160, A2161 A:A119 G:A285, G:A286, U:A287 4dv3 A1852 Pout·4Bout A2235, A2236, A2237, A2238, A2239 G:A266 G:A257, G:A266, U:A256, A:A270 4dv3 A1835 Pout·4Bout A2191, A2192, A2193, A2194, A2195, A2196 A:A766 A:A767, C:A812, A:A768, C:A811 4dv3 A1687 2Pout A2054, A2055, A2268, A2269 G:A1048, U:A1049

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>