MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoy:A1567, See in JSmolClick on the image to toggle views Site type: 2Bout Schematic drawing for 2Bout List of all 555 Mg2+ binding sites with the site type 2Bout 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 23 | « 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 3ofy A1 2Bout A2, A3, A4, A1576, A1577, T87 G:A260, G:A259 3mxh R2 2Bout R734, R735, R736, R737, R738, R739 G:R19, G:R20 3la5 A3 2Bout A104, A106, A110, A114, A356, A382 G:A43, G:A44 1egk C4 2Bout B62, B63, C34, C35, C36, C37 G:C103, G:C102 2r1s A17 2Bout A23, A30, A54, A65, A68, A93 G:A12, C:A11 2r20 A17 2Bout A23, A30, A53, A64, A67, A90 G:A12, C:A11 1hr2 A18 2Bout A359, A360, A361, A362, A363, A364 G:A129, G:A191 1hr2 B19 2Bout B368, B369, B370, B371, B372, B373 G:B129, G:B191 1egk A21 2Bout A28, A29, A30, A31, A32, A33 G:A2, G:A3 1egk A22 2Bout B55, B56, B57, B58, B59, B60 G:A9, DG:B31 1hr2 A22 2Bout A371, A372, A373, A374, A375, A376 G:A242, U:A243 1egk A23 2Bout A34, A35, A36, A37, A38, A39 C:A17, G:A18 1egk A26 2Bout A49, A50, A51, A52, A53, A54 U:A15, G:A16 1egk A27 2Bout A55, A56, A57, A58, A59, A60 G:A13, G:A12 1pjo A35 2Bout A150, A151, A152, A154, B153, B155 A:A4, A:A3 1l2x A52 2Bout A53, A54, A55, A56, A57, A58 G:A4, G:A2 2oiy A98 2Bout A125, A129, A136, A146, A163 U:A6, G:A7 1ik5 B99 2Bout A74, A77, B75, B76, B93 G:B15, G:B16 4g6r B101 2Bout A201, A202, B201, B202, B203, B204 G:B13, G:B12 2oe5 B103 2Bout A109, B105, B106, B107, B108, B110 A:B1490, U:B1489 1y26 X104 2Bout X284, X285, X286, X287, X288, X289 G:X43, G:X44 2oe5 A104 2Bout A111, A112, A113, A114, A115, A116 G:A2, G:A17 3oxj A109 2Bout A138, A139, A140, A141, A142, A143 G:A47, U:A46 3owz B111 2Bout B130, B131, B132, B133, B134, B135 G:B49, G:B50 3oxm A116 2Bout A130, A131, A132, A133, A134, A135 G:A25, G:A26

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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