MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 199 Mg2+ binding sites with the site type 2Pout·3Bout 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 1jj2 08071 2Pout·3Bout 03639, 05598, 06971, 07112, 07385, 07386 A:01815, C:01816 U:01813, C:01818, U:01817 1k73 A8071 2Pout·3Bout A4108, A6060, A7436, A7573, A7849, A7850 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1k8a A8071 2Pout·3Bout A3699, A5624, A6978, A7112, A7387, A7388 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1k9m A8071 2Pout·3Bout A4107, A6058, A7434, A7571, A7848, A7849 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1kc8 A8071 2Pout·3Bout A4116, A6051, A7425, A7561, A7837, A7838 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1kd1 A8071 2Pout·3Bout A4105, A6048, A7421, A7555, A7835, A7836 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1m1k A8071 2Pout·3Bout A3708, A5657, A7015, A7150, A7426, A7427 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1m90 A8071 2Pout·3Bout A3642, A5592, A6955, A7096, A7368, A7369 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1n78 D701 2Pout·3Bout D2323, D2324, D2325, D2326, D2327, D2328 A:D546, G:D522 A:D546, A:D545, C:D509 1n78 C700 2Pout·3Bout C2317, C2318, C2319, C2320, C2321, C2322 A:C546, G:C522 C:C509, A:C545, A:C546 1nji A8071 2Pout·3Bout A4103, A6053, A7417, A7553, A7830, A7831 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1nuj B419 2Pout·3Bout A426, A427, B425, B426, B427, B428 G:A26, A:A25 U:B41, G:B42, G:B43 1nuj H422 2Pout·3Bout G235, G238, H234, H236, H237, H239 G:G26, A:G25 U:H41, G:H42, G:H43 1nuv B412 2Pout·3Bout A421, A422, A423, B428, B429, B430 G:A26, A:A25 U:B41, G:B42, G:B43 1nuv H415 2Pout·3Bout G228, G229, G231, H227, H230, H232 G:G26, A:G25 U:H41, G:H42, G:H43 1q7y A8071 2Pout·3Bout A3620, A5548, A6906, A7040, A7310, A7311 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1q81 A8071 2Pout·3Bout A3622, A5569, A6910, A7049, A7319, A7320 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1q82 A8071 2Pout·3Bout A3624, A5539, A6901, A7035, A7310, A7311 A:A1815, C:A1816 U:A1817, C:A1818, U:A1813 1q86 A8071 2Pout·3Bout A3641, A5571, A6936, A7066, A7340, A7341 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1qvf 08071 2Pout·3Bout 03623, 05541, 06891, 07021, 07286, 07287 A:01815, C:01816 U:01813, C:01818, U:01817 1s72 08071 2Pout·3Bout 03636, 05579, 06933, 07068, 07340, 07341 A:01815, C:01816 U:01813, C:01818, U:01817 1vq4 08071 2Pout·3Bout 04424, 06318, 07618, 07743, 08065, 08066 A:01815, C:01816 U:01813, C:01818, U:01817 1vs5 A1546 2Pout·3Bout A1615, A1616, A1617, A1618, A1619, A1620 G:A803, U:A804 U:A772, G:A773, G:A771 1vs6 B2923 2Pout·3Bout B3104, B3105, B3106, B3107, B3108, B3109 U:B29, A:B447 G:B474, U:B29, G:B30 1vs7 A1547 2Pout·3Bout A1618, A1619, A1620, A1621, A1622, A1623 G:A803, U:A804 U:A772, G:A773, G:A771

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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