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 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" 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 4duz A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 C:A372, G:A376 4duz A1665 Ob·Nb G:A362(N7) A2018, A2019, A2020, A2021 G:A361 4duz A1613 Oph G:A21(OP1) A1930, A1931, A1932 U:A884 4duz A1650 Oph·Pout C:A352(OP2) A1995, A1996, A1997, A1998, A1999 G:A354 G:A331, C:A330, C:A352 A:A59, C:A330, G:A354 4duz A1629 Oph·Pout G:A588(OP2) A1960, A1961, A1962 G:A644 4duz A1814 Oph·Pout G:A750(OP2) A2117, A2118, A2119, A2120, A2121 C:A749 C:A748 G:A752, G:A750 4duz A1649 Oph·Pout G:A903(OP1) A1991, A1992, A1993, A1994 U:A891 4duz A1618 Oph·2Pout A:A768(OP2) A1937, A1938, A1939, A1940 C:A805, U:A804 A:A768, G:A769 4duz A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118 4duz A1844 Bout A2239, A2240, A2241, A2242 G:A700 4duz A1811 3Bout A2107, A2108, A2109, P201 C:A137, G:A138, G:A226 4duz A1770 5Bout A2076, A2077, A2078, A2079, A2080, A2081 G:A664, G:A742, G:A741, G:A666, U:A740 4duz A1816 Pout·3Bout A2128, A2129, A2130, A2131, A2132 U:A871 G:A853, G:A854, G:A852 4duz A1827 Pout·4Bout A2188, A2189, A2190, A2191, A2192 A:A766 U:A813, C:A812, A:A768, C:A811 4duz A1607 2Pout·Bout A1912, A1913, A1914, A1915 U:A652, C:A651 G:A752 4duz A1820 2Pout·2Bout A2148, A2149, A2150, A2151, A2152 A:A119, G:A285 U:A287, G:A286 4duz A1841 2Pout·Rout·2Bout A2223, A2224, A2225, A2226, A2227 C:A1303, U:A1301 G:A1331 G:A1305, G:A1304 4duz A1628 3Pout·Rout A1956, A1957, A1958, A1959 A:A563, U:A560, C:A562 A:A559 4duz A1810 3Pout·Rout A2102, A2103, A2104, A2105, A2106 C:A150, A:A151, G:A168 G:A167 4duz A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617

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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