MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofp A1 2Pout A2, A3, A4, A1576, A1577, T87 G:A259, G:A258 4a1a 05 2Pout 05027, 05028, 05029, 05030, 05031, 05032 G:2137, U:2136 4a1c 070 2Pout 05347, 05348, 05349, 05350, 05351, 05352 A:25, A:24 3v2d 6102 2Pout A5066, A5067, A5068, 8206, 8207 C:A2347, U:A2419 3v27 8102 2Pout A4758, 6201, 8208, 8209, 8210, 8211 C:A2347, U:A2348 4dha 6102 2Pout A4727, 6202, 6203, 6204, 8203, 8204 C:A2347, U:A2348 3owz B114 2Pout B145, B146, B147, B148, B149, B150 A:B11, G:B10 4duy J201 2Pout A2301, J301, J302, J303, N202, N203 A:A1188, C:A1189 3og0 E202 2Pout A3106, A3107, A3108, A3109, A3110, A3111 U:A2016, G:A1256 4dv4 J202 2Pout A2216, I201, J301, J302, N202 C:A1189, A:A1188 4dhc B216 2Pout B335, B336, B337, B338, B339, B340 U:B55, A:B25 2g5k A301 2Pout A416, A417, A419, A420, A421, B418 G:A3, A:B40 2g5k B302 2Pout A424, B422, B423, B425, B426, B427 A:A17, G:B26 4jnx D303 2Pout D405, D406, D407, D408, D409, G504 U:G412, C:G411 2qox N337 2Pout B3290, B3291, B3292, B3293, N339, N340 U:B2818, A:B1652 2i2u A1548 2Pout A1622, A1623, A1624, A1625, A1626, A1627 U:A14, G:A15 2qoy A1559 2Pout A1977, A1978, A1979, A1980, A1981, A1982 U:A13, U:A14 2i2p A1566 2Pout A1718, A1719, A1720, A1721, A1722, A1723 A:A1357, G:A1356 2avy A1566 2Pout A1715, A1716, A1717, A1718, A1719, A1720 A:A1357, G:A1356 1vs5 A1567 2Pout A1717, A1718, A1719, A1720, A1721, A1722 A:A1357, G:A1356 2qow A1571 2Pout A2025, A2026, A2027, A2028, A2029, A2030 U:A552, A:A553 2qp0 A1571 2Pout A2028, A2029, A2030, A2031, A2032, A2033 U:A552, A:A553 2qou A1589 2Pout A2122, A2123, A2124, A2125, A2126, L281 C:A25, A:A553 2i2p A1589 2Pout A1829, A1830, A1831, A1832, A1833, A1834 A:A553, U:A552 2qoy A1589 2Pout A2124, A2125, A2126, A2127, A2128, L1831 A:A553, U:A552

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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