MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 4ji2

4JI2 (3.64Å) -- RIBOSOME : Crystal structure of 30s ribosomal subunit from thermus thermophilus
List of all 23 Mg2+ binding sites in the PDB structure 4ji2 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
4ji2 A1805 Ob G:A610(O6) A2115, A2116, A2117, A2118 A:A608, A:A607 A:A609
4ji2 A1706 Ob G:A1370(O6) A2076, A2077, A2078 U:A1348 U:A1372, C:A1369
4ji2 A1691 Nb G:A324(N7) A2047, A2048, A2049, T201
4ji2 A1685 Ob·Nb G:A362(O6) A2038, A2039, A2040, A2041 G:A361
4ji2 A1721 Ob·2Nb G:A858(O6), G:A869(N7) A2100, A2101, A2102 G:A869
4ji2 A1615 Oph A:A937(OP2) A1935, A1936, A1937, A1938 G:A939, A:A938
4ji2 A1616 Oph G:A21(OP1) A1939, A1940, A1941 A:A573
4ji2 A1663 Oph·Pout C:A352(OP2) A2014, A2015, A2016, A2017 G:A354 G:A331, C:A352 C:A330, A:A59, G:A354
4ji2 A1658 Oph·2Pout A:A1110(OP2) A2006, A2007, A2008 C:A1109, A:A1111 C:A1189, A:A1110, A:A1111
4ji2 A1632 Oph·3Pout U:A560(OP1) A1958, A1959, A1960, A1961 A:A563, G:A557, C:A562 A:A559
4ji2 A1623 Oph·Nb A:A766(OP2) C:A812(N3) A1951, A1952, A1953, A1954 U:A813, C:A811
4ji2 A1606 cis-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117
4ji2 A1634 trans-2Oph G:A588(OP2), G:A644(OP1) A1962, A1963, A1964, A1965 C:A589
4ji2 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510, C:A507 A:A510
4ji2 A1719 trans-2Oph A:A782(OP1), A:A794(OP1) A2096, A2097, A2098 C:A783 C:A1515
4ji2 A1647 Bout A1989, A1990, Q301, Q302 G:A587
4ji2 A1702 Bout A2068, A2069, A2070, A2071 G:A700
4ji2 A1612 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525
4ji2 A1608 2Pout A1913, A1914, A1915, A1916 U:A652, U:A751
4ji2 A1875 2Pout·2Bout A2155, A2156, A2157, A2158, A2159, A2160 A:A609, G:A610 G:A627, G:A628

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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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