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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 4ji3



4JI3 (3.35Å) -- RIBOSOME : Crystal structure of 30s ribosomal subunit from thermus thermophilus
List of all 21 Mg2+ binding sites in the PDB structure 4ji3 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
4ji3 A1701 Ob G:A1370(O6) A2075, A2076, A2077 G:A1371, U:A1372
4ji3 A1689 Nb G:A324(N7) A2049, A2050, A2051, T201 G:A326
4ji3 A1684 Nb G:A362(N7) A2038, A2039, A2040, A2041 G:A361, G:A362
4ji3 A1784 2Ob U:A304(O4), G:A305(O6) A2114, A2115, A2116 G:A293
4ji3 A1714 Ob·2Nb G:A858(O6), G:A869(N7) A2097, A2098, A2099 C:A868, G:A869
4ji3 A1622 Oph A:A766(OP2) A1950, A1951, A1952, A1953 A:A767, U:A813, C:A812, C:A811
4ji3 A1658 Oph·Pout A:A1110(OP2) A2007, A2008, A2009 A:A1111 C:A1189, A:A1111
4ji3 A1634 Oph·2Pout G:A588(OP2) A1962, A1963, A1964, A1965 G:A644, C:A589
4ji3 A1632 Oph·4Pout U:A560(OP2) A1958, A1959, A1960, A1961 C:A562, A:A563, G:A557, G:A558 G:A566
4ji3 A1637 Oph·Nb G:A758(OP2) A1970, A1971, A1972 U:A757 G:A581
4ji3 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510 A:A510
4ji3 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117, U:A118
4ji3 A1611 Bout A1922, A1923, A1924, A1925, A1926 G:A1525
4ji3 A1699 Bout A2068, A2069, A2070, A2071 G:A700
4ji3 A1700 Pout A2072, A2073, A2074, A2123 A:A1204
4ji3 A1698 Pout·2Bout A2065, A2066, A2067, N201 A:A1360 C:A980, A:A1360
4ji3 A1639 Pout·3Bout A1973, A1974, A1975, A1976, A1977 A:A583 G:A584, G:A585, G:A755
4ji3 A1663 Pout·2Rout·3Bout A2015, A2016, A2017, A2018 C:A352 G:A331, C:A352 C:A330, A:A59, G:A354
4ji3 A1612 3Pout·Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617
4ji3 A1608 4Pout A1913, A1914, A1915, A1916 U:A751, C:A651, U:A652, G:A752

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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