MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2982, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·3Bout Schematic drawing for 2Pout·Rout·3Bout List of all 39 Mg2+ binding sites with the site type 2Pout·Rout·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 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v23 A3511 2Pout·Rout·3Bout A4674, A4675, A4676, A4677, A4678 A:A1253, G:A582 C:A1251 G:A585, G:A582, G:A583 4dha A3671 2Pout·Rout·3Bout A4635, A4636, A4637, A4638, A4639, A4640 A:A28, A:A447 A:A447 G:A30, G:A474, U:A29 4gar A3080 2Pout·Rout·3Bout A3573, A3574, A3575, A3576, A3577, 0101 A:A574, C:A2055 A:A2054 U:A2034, G:A2035, A:A574 4peb A3017 2Pout·Rout·3Bout A3283, A3284, A3285, A3286, A3287, A3288 A:A582, A:A1253 C:A1251 G:A583, C:A584, A:A582 4pec A3017 2Pout·Rout·3Bout A3280, A3281, A3282, A3283, A3284, Q301 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582 4tom A3047 2Pout·Rout·3Bout A3412, A3413, A3414, A3415, A3416 G:A1455, A:A1453 C:A1454 G:A1455, G:A1456, U:A1457 4too A3096 2Pout·Rout·3Bout A3635, A3636, A3637, A3638, A3639, A3640 C:A1617, G:A1619 A:A1608 G:A1619, G:A1620, G:A1613 4tox A3097 2Pout·Rout·3Bout A3640, A3641, A3642, A3643, A3644, A3645 A:A1608, G:A1619 A:A1608 G:A1619, G:A1620, G:A1613 4tp3 A3096 2Pout·Rout·3Bout A3636, A3637, A3638, A3639, A3640, A3641 C:A1617, G:A1619 A:A1608 G:A1619, G:A1620, G:A1613 4tp3 A3082 2Pout·Rout·3Bout A3566, A3567, A3568, A3569, A3570, A3571 A:A574, C:A2055 A:A2054 A:A574, G:A2035, U:A2034 4tp5 A3096 2Pout·Rout·3Bout A3645, A3646, A3647, A3648, A3649, A3650 C:A1617, G:A1619 C:A1617 G:A1619, G:A1620, G:A1613 4tp7 A3130 2Pout·Rout·3Bout A3768, A3769, A3770, A3771, A3772, A3773 G:A570, A:A973 A:A972 A:A820, U:A568, A:A821 4tp7 A3039 2Pout·Rout·3Bout A3367, A3368, A3369, A3370, A3371, A3372 A:A2009, U:A1267 G:A1266 A:A2009, G:A2010, U:A2011 4tpf A3130 2Pout·Rout·3Bout A3771, A3772, A3773, A3774, A3775, A3776 G:A570, A:A973 A:A972 A:A820, U:A568, A:A821

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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