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 9 of 12 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dv4 A1629 trans-2Oph G:A588(OP2), G:A644(OP1) A1956, A1957, A1958 4dv5 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118 4dv6 A1660 trans-2Oph G:A506(OP1), A:A509(OP2) A2009, A2010, A2011 A:A510 A:A510 4dv6 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117 4dv7 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117 4ji0 A1634 trans-2Oph G:A588(OP2), G:A644(OP1) A1960, A1961, A1962, A1963 C:A589 4ji0 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510, C:A507 A:A510 4ji1 A1603 trans-2Oph G:A117(OP2), G:A289(OP2) A1903, A1904, A1905, A1906 A:A116, A:A288 G:A117, U:A118 4ji2 A1634 trans-2Oph G:A588(OP2), G:A644(OP1) A1962, A1963, A1964, A1965 C:A589 4ji2 A1719 trans-2Oph A:A782(OP1), A:A794(OP1) A2096, A2097, A2098 C:A783 C:A1515 4ji2 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510, C:A507 A:A510 4ji3 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117, U:A118 4ji3 A1668 trans-2Oph G:A506(OP1), A:A509(OP2) A2019, A2020, A2021 A:A510 A:A510 4ji4 A1717 trans-2Oph A:A782(OP1), A:A794(OP1) A2092, A2093, A2094 C:A783 C:A1515 4ji7 A1653 trans-2Oph G:A506(OP1), A:A509(OP2) A2196, A2197, A2198 A:A510 A:A510 4ji7 A1603 trans-2Oph G:A117(OP2), G:A289(OP2) A2104, A2105, A2106, A2107 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 4kix A3023 trans-2Oph A:A751(OP1), A:A1614(OP1) A3307, A3308, A3309, A3310 G:A1613 A:A789, A:A751, A:A1614, C:A1617 4kiz A3078 trans-2Oph G:A370(OP2), A:A422(OP2) A3551, A3553 C:A421 G:A370, A:A422 4kj3 A3022 trans-2Oph A:A751(OP1), A:A1614(OP1) A3307, A3308, A3309 A:A751, A:A789, C:A1617, A:A1614, C:A1615 4kj5 A3072 trans-2Oph C:A2579(OP1), C:A2611(OP2) A3539, A3540 U:A2580 4kjb A3022 trans-2Oph A:A751(OP1), A:A1614(OP1) A3309, A3310, A3311, A3312 G:A1613 A:A751, C:A1617, A:A1614, C:A1615, A:A789 4nvv A3440 trans-2Oph C:A1344(OP2), U:A1686(OP2) A4429, A4430, A4431, A4432 C:A1685, C:A1343 C:A2722 G:A1345 4nvv A3418 trans-2Oph U:A834(OP1), C:A837(OP2) A4366, A4367, A4368, A4369 A:A836 A:A1811 4nvv A3336 trans-2Oph G:A397(OP2), A:A449(OP2) A4153, A4154, A4155, A4156 G:A397, A:A449, C:A286, A:A450

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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