`

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

Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 2qow




2QOW (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 30s subunit of the second 70s ribosome, with spectinomycin bound. the entire crystal structure contains two 70s ribosomes.
List of all 54 Mg2+ binding sites in the PDB structure 2qow 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
2qow A1583 Or C:A934(O5') A2083, A2084, A2085, A2086, A2087 C:A934, U:A1345
2qow A1594 Ob G:A1370(O6) A2138, A2139, A2140, A2141, A2142 U:A1372, U:A1351, G:A1371
2qow A1581 Ob G:A1417(O6) A2072, A2073, A2074, A2075, A2076 G:A1416, G:A1415 G:A1482, G:A1416
2qow A1549 Nb G:A362(N7) A1913, A1914, A1915, L124, L1633 G:A361 G:A361
2qow A1567 Nb G:A324(N7) A2005, A2006, A2007, A2008, A2009 U:A323, G:A326
2qow A1569 Oph A:A608(OP2) A2014, A2015, A2016, A2017, A2018 A:A630, A:A609, C:A631, U:A610
2qow A1562 Oph G:A21(OP1) A1983, A1984, A1985, A1986, A1987 G:A567, G:A568 A:A573, A:A563
2qow A1578 Oph·Pout C:A352(OP2) A2056, A2057, A2058, A2059, A2060 G:A354 C:A330, C:A352 C:A330, G:A354, A:A59
2qow A1586 Oph·Pout A:A937(OP2) A2095, A2096, A2097, A2098, A2099 A:A938 A:A938, G:A939
2qow A1543 Oph·Pout U:A891(OP2) A1884, A1885, A1886, A1887, A1888 A:A892 U:A905, U:A904
2qow A1573 Oph·Pout G:A100(OP2) A2034, A2035, A2036, A2037, A2038 A:A101 G:A64, A:A101
2qow A1565 Oph·Pout A:A1433(OP2) A1996, A1997, A1998, A1999, A2000 A:A1434 A:A1434, G:A1435
2qow A1561 Oph·Pout A:A572(OP1) A1978, A1979, A1980, A1981, A1982 A:A573 A:A819
2qow A1600 Oph·Pout U:A1224(OP1) A2162, A2163, A2164, A2165, A2166 U:A952 C:A1223 A:A977
2qow A1547 Oph·2Pout A:A560(OP2) A1902, A1903, A1904, A1905, A1906 A:A563, U:A562 U:A565, G:A566
2qow A1597 Oph·2Pout A:A1110(OP2) A2149, A2150, A2151, A2152, A2153 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111
2qow A1595 Oph·2Pout U:A1199(OP1) A2143, A2144, A2145, A2146 A:A964, G:A1198
2qow A1553 Oph·2Pout C:A578(OP1) A1931, A1932, A1933, A1934, A1935 C:A576, C:A817
2qow A1576 Oph·3Pout C:A536(OP1) A2048, A2049, A2050, A2051, A2052 G:A537, A:A523, C:A503 C:A522
2qow A1575 Oph·Ob A:A195(OP2) U:A180(O4) A2045, A2046, A2047, T1759 C:A194, C:A178, A:A179 A:A181

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>