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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 2qou



2QOU (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 30s subunit of the first 70s ribosome, with spectinomycin bound. the entire crystal structure contains two 70s ribosomes.
List of all 55 Mg2+ binding sites in the PDB structure 2qou 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qou A1547 Or C:A934(O5') A1917, A1918, A1919, A1920, A1921 U:A1345, C:A934
2qou A1575 Ob G:A1370(O6) A2058, A2059, A2060, A2061, A2062 U:A1351, G:A1371
2qou A1602 Ob G:A1417(O6) A2185, A2186, A2187, A2188, A2189 G:A1416, G:A1415 G:A1416, G:A1482
2qou A1601 Ob U:A1358(O4) A2180, A2181, A2182, A2183, A2184 A:A1357 C:A1359, A:A1357, G:A976
2qou A1561 Ob G:A1050(O6) A1985, A1986, A1987, A1988, A1989 G:A1207, C:A1051, G:A1048
2qou A1581 Nb G:A324(N7) A2084, A2085, A2086, A2087, A2088 G:A326
2qou A1560 Nb G:A362(N7) A1980, A1981, A1982, A1983, A1984 G:A362, A:A364 G:A361
2qou A1571 Oph G:A21(OP1) A2039, A2040, A2041, A2042, A2043 G:A567, A:A573, A:A563
2qou A1570 Oph A:A572(OP1) A2034, A2035, A2036, A2037, A2038 A:A819
2qou A1583 Oph A:A608(OP2) A2093, A2094, A2095, A2096, A2097 C:A631, A:A609, U:A610
2qou A1554 Oph·Pout A:A937(OP2) A1949, A1950, A1951, A1952, A1953 A:A938 A:A938, A:A937, G:A939
2qou A1596 Oph·Pout C:A352(OP2) A2152, A2153, A2154, A2155, A2156 G:A354 G:A331, C:A330, C:A352 C:A330, A:A59, G:A354
2qou A1591 Oph·Pout G:A100(OP2) A2130, A2131, A2132, A2133, A2134 A:A101 G:A64, G:A100, A:A101
2qou A1578 Oph·Pout A:A1433(OP2) A2069, A2070, A2071, A2072, A2073 A:A1434 A:A1434, G:A1435
2qou A1597 Oph·2Pout G:A111(OP2) A2157, A2158, A2159, A2160, A2161 G:A112, C:A110 G:A112, G:A111
2qou A1587 Oph·2Pout U:A1224(OP1) A2111, A2112, A2113, A2114, A2115 U:A952, G:A951
2qou A1572 Oph·3Pout G:A115(OP1) A2044, A2045, A2046, A2047 C:A48, U:A49, A:A51
2qou A1543 Oph·3Pout C:A578(OP1) A1897, A1898, A1899, A1900, A1901 C:A576, C:A817, U:A820 G:A575
2qou A1549 Oph·4Pout A:A560(OP2) A1928, A1929, A1930, A1931, A1932 U:A562, A:A563, G:A557, G:A558 A:A559
2qou A1582 Oph·Ob A:A533(OP1) U:A516(O4) A2089, A2090, A2091, A2092 A:A532 G:A515, G:A517

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>