MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qov:B2933, See in JSmolClick on the image to toggle views Site type: Oph·3Pout Schematic drawing for Oph·3Pout List of all 867 Mg2+ binding sites with the site type Oph·3Pout 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 35 | « 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 3la5 A5 Oph·3Pout U:A68(OP1) A147, A155, A378, A435 C:A26, C:A27, G:A37 1hr2 A7 Oph·3Pout A:A171(OP2) A332, A333, A334, A335, A336 C:A165, C:A170, U:A168 U:A167 A:A171, U:A167 1hr2 B8 Oph·3Pout A:B171(OP2) B336, B337, B338, B339, B340 C:B170, C:B165, U:B168 U:B167 A:B171, U:B167 3owi A111 Oph·3Pout U:A20(OP2) A167, A168, A169, A170, A171 A:A21, C:A15, G:B25 C:B24 3oww A111 Oph·3Pout U:A20(OP2) A167, A168, A169, A170, A171 A:A21, C:A15, G:B25 C:B24 3owz B112 Oph·3Pout C:B24(OP1) B136, B137, B138, B139, B140 G:B73, C:B74, G:B25 A:A76 A:A76, A:B77 3oxd A112 Oph·3Pout U:A20(OP2) A163, A164, A165, A166, A167 A:A21, C:A15, G:B25 C:B24, U:A19 3ox0 A112 Oph·3Pout U:A20(OP2) A152, A153, A154, A155, A156 A:A21, C:A15, G:B25 C:B24 4jf2 A117 Oph·3Pout U:A41(OP1) A312, A313, A314, A315, A316 G:A23, A:A24, A:A55 U:A53 4jf2 A119 Oph·3Pout G:A42(OP1) A326, A327, A328, A329, A330 G:A23, A:A43, C:A22 3i1s A1539 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A575 3i1o A1539 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A575, G:A821 3i21 A1539 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A575, G:A821 3ofa A1540 Oph·3Pout A:A560(OP2) A1607, A1608, A1609, A1610, A1611 U:A562, A:A563, G:A557 A:A559 G:A566 3ofo A1540 Oph·3Pout A:A560(OP2) A1606, A1607, A1608, A1609, A1610 G:A557, U:A562, A:A563 A:A559 U:A565, G:A566 3ora A1540 Oph·3Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 A:A563, U:A562, G:A557 A:A559 G:A566 3oar A1542 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A821 3ofx A1542 Oph·3Pout C:A578(OP1) A1615, A1616, A1617, A1618, A1619 C:A576, C:A817, U:A820 G:A575 3oaq A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 G:A575 3ofb A1542 Oph·3Pout C:A578(OP1) A1612, A1613, A1614, A1615, A1616 C:A576, C:A817, U:A820 G:A575, G:A821 3ora A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 3or9 A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 G:A575 3ofa A1542 Oph·3Pout C:A578(OP1) A1615, A1616, A1617, A1618, A1619 C:A576, C:A817, U:A820 G:A575 3i1q A1542 Oph·3Pout C:A578(OP1) A1613, A1614, A1615, A1616, A1617 C:A576, C:A817, U:A820 G:A575 3i1z A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 G:A575

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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