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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 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"
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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
2qow A1565 Oph·Pout A:A1433(OP2) A1996, A1997, A1998, A1999, A2000 A:A1434 A:A1434, G:A1435
2qow A1566 Oph·Ob G:A558(OP1) G:A299(O6) A2001, A2002, A2003, A2004 A:A560 G:A297 A:A298, G:A566
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 A1570 2Bout A2019, A2020, A2021, A2022, A2023, A2024 G:A1525, G:A1526
2qow A1571 2Pout A2025, A2026, A2027, A2028, A2029, A2030 U:A552, A:A553
2qow A1573 Oph·Pout G:A100(OP2) A2034, A2035, A2036, A2037, A2038 A:A101 G:A64, A:A101
2qow A1574 2Bout A2039, A2040, A2041, A2042, A2043, A2044 G:A38, U:A37
2qow A1575 Oph·Ob A:A195(OP2) U:A180(O4) A2045, A2046, A2047, T1759 C:A194, C:A178, A:A179 A:A181
2qow A1576 Oph·3Pout C:A536(OP1) A2048, A2049, A2050, A2051, A2052 G:A537, A:A523, C:A503 C:A522
2qow A1577 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2053, A2054, A2055 A:A288 G:A117, U:A118
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 A1579 Pout·2Bout A2061, A2062, A2063, A2064, A2065 G:A111 G:A112, G:A113
2qow A1580 Pout·2Bout A2066, A2067, A2068, A2069, A2070, A2071 G:A259 G:A259, G:A260
2qow A1581 Ob G:A1417(O6) A2072, A2073, A2074, A2075, A2076 G:A1416, G:A1415 G:A1482, G:A1416
2qow A1582 Pout·Bout A2077, A2078, A2079, A2080, A2081, A2082 G:A1079 G:A1077
2qow A1583 Or C:A934(O5') A2083, A2084, A2085, A2086, A2087 C:A934, U:A1345
2qow A1584 cis-2Oph C:A1054(OP2), A:A1197(OP2) A2088, A2089, A2090, A2091 G:A1053 G:A1198, A:A1197
2qow A1585 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2092, A2093, A2094
2qow A1586 Oph·Pout A:A937(OP2) A2095, A2096, A2097, A2098, A2099 A:A938 A:A938, G:A939

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>