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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 4duy



4DUY (3.39Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c
List of all 37 Mg2+ binding sites in the PDB structure 4duy 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
4duy A1693 Ob G:A1370(O6) A2064, A2065, A2066 G:A1371
4duy A1672 Nb G:A362(N7) A2028, A2029, A2030, A2031 G:A361, G:A362
4duy A1679 Nb G:A324(N7) A2039, A2040, A2041, A2042 G:A326
4duy A1620 Oph A:A766(OP2) A1950, A1951, A1952, A1953 A:A767, U:A813, C:A812, C:A811
4duy A1806 Oph·Pout U:A81(OP2) A2196, A2197, A2198, A2199 U:A82
4duy A1613 Oph·Pout A:A937(OP2) A1935, A1936, A1937, A1938 A:A938 A:A938, A:A937, G:A939
4duy A1650 Oph·Pout A:A1110(OP2) A1999, A2000, A2001 A:A1111 C:A1189, A:A1111
4duy A1654 Oph·Pout C:A352(OP2) A2007, A2008, A2009, A2010 G:A354 C:A352 C:A330, A:A59, G:A354
4duy A1704 Oph·2Pout A:A794(OP1) A2083, A2084, A2085 A:A782, C:A783 C:A1515 C:A1515
4duy A1629 Oph·3Pout G:A588(OP2) A1960, A1961, A1962, A1963 C:A645, G:A644, C:A589
4duy A1627 Oph·4Pout U:A560(OP2) A1956, A1957, A1958, A1959 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4duy A1605 cis-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117
4duy A1658 trans-2Oph G:A506(OP1), A:A509(OP2) A2012, A2013, A2014 A:A510 A:A510
4duy A1690 Bout A2057, A2058, A2059, A2060 G:A700
4duy A1641 Bout A1985, A1986, A1987, A1988 G:A587
4duy A1836 2Bout A2307, A2308, A2309, A2310, A2311 G:A709, G:A710
4duy A1854 3Bout A2379, A2380, A2381, A2382 G:A734, U:A672, G:A671
4duy A1828 3Rout·4Bout A2283, A2284, A2285, A2286 G:A953, U:A952, C:A1230 A:A969, C:A970, U:A952, C:A1230
4duy A1820 Pout·3Bout A2249, A2250, A2251, A2252, A2253, A2254 C:A980 U:A1219, G:A1220, G:A1221
4duy A1790 Pout·3Bout A2132, A2133, A2134, A2135, A2136, A2137 U:A871 G:A853, G:A854, G:A852

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>