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 1egk A22 2Bout B55, B56, B57, B58, B59, B60 G:A9, DG:B31 1egk C4 2Bout B62, B63, C34, C35, C36, C37 G:C103, G:C102 1egk A21 2Bout A28, A29, A30, A31, A32, A33 G:A2, G:A3 1egk A26 2Bout A49, A50, A51, A52, A53, A54 U:A15, G:A16 1egk A23 2Bout A34, A35, A36, A37, A38, A39 C:A17, G:A18 1egk A27 2Bout A55, A56, A57, A58, A59, A60 G:A13, G:A12 1hr2 A22 2Bout A371, A372, A373, A374, A375, A376 G:A242, U:A243 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 1ik5 B99 2Bout A74, A77, B75, B76, B93 G:B15, G:B16 1jj2 08063 2Bout 03708, 06551, 06986, 07311, 07387, 07440 G:01364, G:01363 1k73 A8063 2Bout A4177, A7016, A7450, A7775, A7851, A7904 G:A1364, G:A1363 1k8a A8063 2Bout A3767, A6567, A6993, A7313, A7389, A7440 G:A1364, G:A1363 1k9m A8063 2Bout A4174, A7013, A7448, A7772, A7850, A7901 G:A1364, G:A1363 1kc8 A8063 2Bout A4183, A7005, A7439, A7761, A7839, A7891 G:A1364, G:A1363 1kd1 A8063 2Bout A4175, A7001, A7436, A7758, A7837, A7889 G:A1364, G:A1363 1kqs 08063 2Bout 03686, 06502, 06927, 07246, 07322, 07373 G:01364, G:01363 1l2x A52 2Bout A53, A54, A55, A56, A57, A58 G:A4, G:A2 1m90 A8063 2Bout A3713, A6540, A6971, A7293, A7370, A7423 G:A1364, G:A1363 1nji A8063 2Bout A4171, A7001, A7431, A7753, A7832, A7886 G:A1364, G:A1363 1o3z B304 2Bout B566, B577, B599, B600, B601 G:B4, U:B3 1o3z B305 2Bout B519, B558, B559, B567, B574, B586 G:B7, U:B6 1pjo A35 2Bout A150, A151, A152, A154, B153, B155 A:A4, A:A3 1q7y A8063 2Bout A3687, A6496, A6922, A7236, A7312, A7363 G:A1364, G:A1363 1q81 A8063 2Bout A3691, A6500, A6926, A7244, A7321, A7373 G:A1364, G:A1363

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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