MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 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 5 of 14 | « 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 2qoz B2918 3Bout B3570, B3571, B3572, B3573, B3574, B3575 U:B18, U:B521, G:B17 2qp0 A1591 3Bout A2118, A2119, A2120, A2121, E293, E1834 G:A11, U:A12, G:A22 2qp1 B2956 3Bout B3767, B3768, B3769, B3770, B3771, B3772 U:B434, A:B42, G:B43 2qp1 B2969 3Bout B3835, B3836, B3837, B3838, B3839, B3840 U:B1258, G:B1259, U:B580 2qp1 B2965 3Bout B3814, B3815, B3816, B3817, B3818, B3819 G:B17, U:B18, U:B521 2z4k A1568 3Bout A1724, A1725, A1726, A1727, A1728, A1729 G:A377, G:A378, G:A376 2z4l B2919 3Bout B3075, B3076, B3077, B3078, B3079, B3080 U:B521, U:B18, G:B17 2z4m A1567 3Bout A1715, A1716, A1717, A1718, A1719, A1720 G:A257, G:A258, G:A259 2z4m A1591 3Bout A1836, A1837, A1838, A1839, A1840, A1841 G:A1525, G:A1526, C:A1524 2z4n B2957 3Bout B3263, B3264, B3265, B3266, B3267, B3268 A:B42, G:B43, U:B434 2z4n B2953 3Bout B3245, B3246, B3247, B3248, B3249, B3250 G:B2549, G:B2550, G:B2557 3cgs B1 3Bout A13, A14, B26, B27, B28, B29 G:B20, G:A5, U:B19 3df2 B3240 3Bout B4241, B4242, B4243, B4244, B4245 G:B2303, U:B2302, G:B2304 3df2 B3014 3Bout B4015, B4016, B4017, B4018, B4019, B4020 U:B580, A:B1260, U:B1258 3df2 B3078 3Bout B4079, B4080, B4081, B4082, B4083, B4084 U:B521, G:B17, U:B18 3df2 B3464 3Bout B4465, B4466, B4467, B4468, B4469, B4470 G:B2549, G:B2550, G:B2557 3df3 A2141 3Bout A4142, A4143, A4144, A4145, A4146, A4147 G:A257, G:A258, G:A259 3df4 B3357 3Bout B4358, B4359, B4360, B4361, B4362, B4363 G:B17, U:B18, U:B521 3df4 B3301 3Bout B4302, B4303, B4304, B4305, B4306, B4307 A:B42, G:B43, U:B434 3df4 B3279 3Bout B4280, B4281, B4282, B4283, B4284, B4285 G:B2549, G:B2550, G:B2557 3hax E200 3Bout E401, E402, E403, E404, E405, E406 G:E20, G:E21, G:E22 3hhn C137 3Bout C136, C138, C139, C140, C141, C142 G:C18, G:C17, U:C16 3hhn E130 3Bout E129, E131, E132, E133, E134, E135 G:E18, U:E16, G:E17 3hhn C123 3Bout C122, C124, C125, C126, C127, C128 G:C2, G:C1, A:C-1 3hhn C1025 3Bout C1057, C1058, C1059, C1060, C1061, C1062 G:C87, G:C88, A:C103

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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