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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 2qp0



2QP0 (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 second 70s ribosome, with spectinomycin and neomycin bound. the entire crystal structure contains two
List of all 57 Mg2+ binding sites in the PDB structure 2qp0 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
2qp0 A1581 Ob G:A1417(O6) A2071, A2072, A2073, A2074, A2075 G:A1415, G:A1416 G:A1482, G:A1416
2qp0 A1549 Nb G:A362(N7) A1914, A1915, A1916, A1917, A1918 G:A361, G:A362 G:A361
2qp0 A1567 Nb G:A324(N7) A2008, A2009, A2010, A2011, A2012 U:A323, G:A326
2qp0 A1564 2Nb G:A858(N7), G:A869(N7) A1995, A1996, A1997, A1998 G:A869, G:A858, C:A868
2qp0 A1561 Oph A:A572(OP1) A1981, A1982, A1983, A1984, A1985 A:A819
2qp0 A1586 Oph A:A937(OP2) A2093, A2094, A2095, A2096, A2097 A:A938, G:A939
2qp0 A1562 Oph G:A21(OP1) A1986, A1987, A1988, A1989, A1990 G:A568, G:A567 A:A573, G:A567
2qp0 A1565 Oph·Pout A:A1433(OP2) A1999, A2000, A2001, A2002, A2003 A:A1434 G:A1432 A:A1434, G:A1435
2qp0 A1583 Oph·Pout C:A934(OP1) A2081, A2082, A2083, A2084, A2085 U:A1345 U:A1345
2qp0 A1579 Oph·Pout G:A111(OP2) A2060, A2061, A2062, A2063, A2064 C:A110 G:A112, G:A111, G:A113
2qp0 A1578 Oph·Pout C:A352(OP2) A2055, A2056, A2057, A2058, A2059 G:A354 C:A352, C:A330 C:A330, G:A354, A:A59
2qp0 A1573 Oph·Pout G:A100(OP2) A2037, A2038, A2039, A2040, A2041 A:A101 G:A64, G:A100, A:A101
2qp0 A1569 Oph·Pout A:A608(OP2) A2017, A2018, A2019, A2020, A2021 A:A607 G:A292 A:A630, A:A609, C:A631, U:A610
2qp0 A1598 Oph·2Pout A:A1110(OP2) A2151, A2152, A2153, A2154, A2155 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111
2qp0 A1547 Oph·2Pout A:A560(OP2) A1903, A1904, A1905, A1906, A1907 U:A562, A:A563 A:A559 U:A565, G:A566
2qp0 A1601 Oph·2Pout U:A1224(OP1) A2164, A2165, A2166, A2167, A2168 G:A951, U:A952 C:A1223 A:A977
2qp0 A1543 Oph·2Pout U:A891(OP2) A1885, A1886, A1887, A1888, A1889 A:A892, U:A904 U:A905, U:A904
2qp0 A1553 Oph·3Pout C:A578(OP1) A1934, A1935, A1936, A1937, A1938 C:A576, C:A817, U:A820 G:A575
2qp0 A1576 Oph·4Pout C:A536(OP1) A2047, A2048, A2049, A2050, A2051 C:A504, G:A537, A:A523, C:A503 C:A522
2qp0 A1575 Oph·Ob A:A195(OP2) U:A180(O4) A2043, A2044, A2045, A2046 C:A194, 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>