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 3v2e 3V2E (2.7Å) -- RIBOSOME/INHIBITOR : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound yfia of the 2nd ribosome in the asu List of all 20 Mg2+ binding sites in the PDB structure 3v2e 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 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v2e A1747 Or U:A1364(O2') A2159, A2160, A2161, A2162 A:A949, G:A1233, G:A1365 G:A971, U:A1364, A:A949, G:A1233 3v2e A1741 Nb G:A324(N7) A2143, A2144, T201, T202 U:A323 3v2e A1764 Nb G:A362(N7) A2201, A2202, A2203, A2204 G:A361, G:A362 G:A361 3v2e A1718 Oph A:A937(OP2) A2089, A2090, A2091, A2092 G:A939 3v2e A1701 Oph C:A770(OP1) A2047, A2048, A2049, A2050 3v2e A1660 Oph·Pout A:A608(OP2) A1939, A1940, A1941, A1942 A:A607 G:A610, A:A608, A:A609 3v2e A1703 Oph·2Pout A:A768(OP2) A2055, A2056, A2057, A2058 A:A767, C:A805 G:A769, A:A768 3v2e A1694 Oph·4Pout U:A560(OP2) A2025, A2026, A2027, A2028 C:A562, A:A563, G:A557, G:A558 A:A559 3v2e A1742 Oph·Ob A:A197(OP2) G:A145(O6) A2145, A2146, A2147, A2148 A:A196 G:A144, A:A196, G:A146 3v2e A1666 Oph·Ob C:A352(OP2) C:A330(O2) A1952, A1953, A1954, A1955 G:A354 C:A352, G:A331, C:A330 A:A59 3v2e A1667 cis-2Oph A:A109(OP1), G:A331(OP2) A1956, A1957, A1958, A1959 G:A111, G:A331 3v2e A1684 2Bout A2001, A2002, A2003, A2004, A2005 G:A285, U:A287 3v2e A1797 2Bout A2285, A2286, A2287, A2288 G:A1471, G:A1469 3v2e A1697 3Bout A2036, A2037, A2038, A2039, A2040 G:A126, G:A127, U:A125 3v2e A1733 3Bout A2125, A2126, A2127, A2128 G:A376, G:A377, U:A375 3v2e A1756 Pout·2Bout A2180, A2181, A2182, A2183 G:A610 G:A627, G:A628 3v2e A1796 Pout·2Bout A2281, A2282, A2283, A2284 A:A781 G:A800, G:A799 3v2e A1768 2Pout·Bout A2214, A2215, A2216, A2217 A:A374, G:A384 A:A453 3v2e A1690 2Pout·2Bout A2012, A2013, A2014, A2015, A2016 G:A265, G:A266 G:A258, G:A259 3v2e A1798 3Pout A2289, A2290, A2291, A2292 G:A568, A:A864, U:A863

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].

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