MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3q3z:A6, See in JSmolClick on the image to toggle views Site type: trans-2Oph Schematic drawing for trans-2Oph List of all 282 Mg2+ binding sites with the site type trans-2Oph in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 1 of 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3q3z A6 trans-2Oph U:A60(OP1), U:A66(OP1) A95, A96, A101, A102 A:A61 3q3z V83 trans-2Oph U:V60(OP1), U:V66(OP1) V171, V172, V173, V174 A:V61 3oww A103 trans-2Oph A:A22(OP1), A:A75(OP2) A138, A139, A140, A141 C:A74 A:A75 3owi A103 trans-2Oph A:A22(OP1), A:A75(OP2) A139, A140, A141, A142 C:A74 A:A75 3v2f B208 trans-2Oph C:B30(OP1), A:B46(OP1) B323, B324, B325, B326 C:B31 462d B502 trans-2Oph G:A9(OP1), G:B9(OP1) A565, A597, B571, B594 G:A10, G:B10 3hhn E1021 trans-2Oph C:E70(OP1), U:E106(OP1) E1039, E1040, E1041, E1042 G:E72 A:E71 3hhn C1021 trans-2Oph C:C70(OP1), U:C106(OP1) C1037, C1038, C1039, C1040 G:C72 A:C71 3oar A1545 trans-2Oph G:A577(OP2), A:A814(OP2) A1628, A1629, A1630, A1631 A:A815 4ji7 A1603 trans-2Oph G:A117(OP2), G:A289(OP2) A2104, A2105, A2106, A2107 A:A116, A:A288 G:A117, U:A118 4ji1 A1603 trans-2Oph G:A117(OP2), G:A289(OP2) A1903, A1904, A1905, A1906 A:A116, A:A288 G:A117, U:A118 4ji8 A1604 trans-2Oph G:A117(OP2), G:A289(OP2) A2004, A2005, A2006, A2007 A:A116, A:A288 G:A115 G:A117 4dv7 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117 4dv6 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117 4dv3 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117 4duz A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118 4dr5 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1915, A1916, A1917, A1918 A:A116, A:A288 G:A117 4dv5 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118 4ji3 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117, U:A118 4dv2 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117, U:A118 4dr6 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A2015, A2016, A2017, A2018 A:A116, A:A288 G:A117 4dr3 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1910, A1911, A1912, A1913 A:A116, A:A288 G:A117 4dr2 A1623 trans-2Oph G:A117(OP2), G:A289(OP2) A2017, A2018, A2019, A2020 A:A116, A:A288 G:A117 4dr4 A1624 trans-2Oph G:A117(OP2), G:A289(OP2) A2014, A2015, A2016, A2017 A:A116, A:A288 G:A117, U:A118 4dv4 A1629 trans-2Oph G:A588(OP2), G:A644(OP1) A1956, A1957, A1958

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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