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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 4ji0



4JI0 (3.49Å) -- RIBOSOME : Crystal structure of 30s ribosomal subunit from thermus thermophilus
List of all 24 Mg2+ binding sites in the PDB structure 4ji0 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
4ji0 A1713 Ob G:A258(O6) A2092, A2093, A2094, A2095 G:A265, G:A266 G:A259, G:A257
4ji0 A1706 Ob G:A1370(O6) A2078, A2079, A2080 G:A1371, U:A1372
4ji0 A1691 Nb G:A324(N7) A2048, A2049, A2050, A2051
4ji0 A1616 Oph G:A21(OP1) A1939, A1940, A1941 G:A567, A:A573
4ji0 A1615 Oph A:A937(OP2) A1935, A1936, A1937, A1938 A:A937, A:A938, G:A939
4ji0 A1663 Oph·Pout C:A352(OP2) A2014, A2015, A2016, A2017 G:A354 G:A331, C:A352 C:A330, A:A59, G:A354
4ji0 A1658 Oph·Pout A:A1110(OP2) A2007, A2008, C401 C:A1109 A:A1111, C:A1189
4ji0 A1632 Oph·4Pout U:A560(OP1) A1956, A1957, A1958, A1959 A:A563, G:A557, G:A558, C:A562 A:A559
4ji0 A1623 Oph·Nb A:A766(OP2) C:A812(N3) A1949, A1950, A1951, A1952 U:A813, C:A811
4ji0 A1606 cis-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117
4ji0 A1717 cis-2Oph A:A782(OP1), A:A794(OP1) A2098, A2099, A2100 C:A783 C:A1515, G:A1521
4ji0 A1634 trans-2Oph G:A588(OP2), G:A644(OP1) A1960, A1961, A1962, A1963 C:A589
4ji0 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510, C:A507 A:A510
4ji0 A1703 Bout A2070, A2071, A2072, A2073 G:A700
4ji0 A1612 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525
4ji0 A1815 Pout·2Bout A2131, A2132, A2133, A2134, A2135, A2136 C:A398 C:A36, U:A37
4ji0 A1639 Pout·2Bout A1971, A1972, A1973, A1974, A1975 A:A583 G:A584, G:A585
4ji0 A1701 Pout·4Bout A2066, A2067, A2068, A2069 A:A1360 C:A980, C:A979, A:A1360, G:A1361
4ji0 A1608 2Pout·Bout A1913, A1914, A1915, A1916 U:A751, U:A652 G:A752
4ji0 A1794 2Pout·2Bout A2116, A2117, A2118, A2119 A:A608, A:A607 G:A610, A:A609

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/)
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