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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 2qoy



2QOY (3.5Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin and neomycin. this file contains the 30s subunit of the first 70s ribosome, with spectinomycin and neomycin bound. the entire crystal structure contains two
List of all 58 Mg2+ binding sites in the PDB structure 2qoy 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
2qoy A1602 Ob G:A1417(O6) A2187, A2188, A2189, A2190, A2191 G:A1416, G:A1415 G:A1482, G:A1416
2qoy A1575 Ob G:A1370(O6) A2060, A2061, A2062, A2063, A2064 U:A1348 U:A1351, A:A1350, G:A1371, U:A1372
2qoy A1561 Ob G:A1050(O6) A1987, A1988, A1989, A1990, A1991 U:A1049 G:A1048
2qoy A1560 Nb G:A362(N7) A1983, A1984, A1985, A1986, L1690 G:A362
2qoy A1581 Nb G:A324(N7) A2086, A2087, A2088, A2089, A2090 U:A323, G:A326
2qoy A1573 2Nb G:A858(N7), G:A869(N7) A2050, A2051, A2052, A2053 G:A858, G:A869, C:A868
2qoy A1591 Oph G:A100(OP2) A2132, A2133, A2134, A2135, A2136 G:A64
2qoy A1596 Oph C:A352(OP2) A2154, A2155, A2156, A2157, A2158 C:A330, G:A331, C:A352 A:A59, C:A330, G:A354
2qoy A1578 Oph·Pout A:A1433(OP2) A2071, A2072, A2073, A2074, A2075 A:A1434 A:A1434, G:A1435
2qoy A1571 Oph·Pout G:A21(OP1) A2041, A2042, A2043, A2044, A2045 U:A561 G:A568, G:A567 A:A573, G:A567
2qoy A1570 Oph·Pout A:A572(OP1) A2036, A2037, A2038, A2039, A2040 G:A917 A:A819
2qoy A1569 Oph·Pout A:A768(OP2) A2031, A2032, A2033, A2034, A2035 U:A804 G:A769
2qoy A1554 Oph·Pout A:A937(OP2) A1951, A1952, A1953, A1954, A1955 A:A938 A:A938, G:A939
2qoy A1583 Oph·Pout A:A608(OP2) A2095, A2096, A2097, A2098, A2099 A:A609 A:A630, C:A631, A:A609, U:A610
2qoy A1547 Oph·Pout C:A934(OP1) A1919, A1920, A1921, A1922, A1923 U:A1345
2qoy A1597 Oph·Pout G:A111(OP2) A2159, A2160, A2161, A2162, A2163 C:A110 G:A112, G:A111
2qoy A1584 Oph·2Pout A:A1110(OP2) A2100, A2101, A2102, A2103, A2104 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111
2qoy A1587 Oph·2Pout U:A1224(OP1) A2113, A2114, A2115, A2116, A2117 G:A951, U:A952 A:A977
2qoy A1543 Oph·3Pout C:A578(OP1) A1899, A1900, A1901, A1902, A1903 C:A576, C:A817, U:A820 G:A575
2qoy A1549 Oph·4Pout A:A560(OP2) A1930, A1931, A1932, A1933, A1934 U:A562, A:A563, G:A557, G:A558 A:A559

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>