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 4 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 2qao B3396 3Bout B3945, B3946, B3947, B3948, B3949, B3950 A:B739, G:B757, A:B756 3v27 A3395 3Bout A4205, A4206, A4207, A4208, A4209 G:A710, C:A720, U:A709 3v25 A3395 3Bout A4054, A4055, A4056, A4057 G:A496, G:A494, G:A495 3v25 A3385 3Bout A4024, A4025, A4026, A4027 G:A259, U:A239, G:A258 2qbc B3382 3Bout B3931, B3932, B3933, B3934, B3935, B3936 G:B1259, A:B1260, U:B580 3v27 A3381 3Bout A4146, A4147, A4148, A4149, A4150, A4151 G:A1485, G:A1482, G:A1484 3v27 A3380 3Bout A4141, A4142, A4143, A4144, A4145 A:A1486, G:A1487, G:A1488 4nw1 A3374 3Bout A4351, A4352, A4353, A4354 G:A2494, G:A2455, G:A2495 3df4 B3357 3Bout B4358, B4359, B4360, B4361, B4362, B4363 G:B17, U:B18, U:B521 3v25 A3309 3Bout A3779, A3780, A3781, A3782, A3783, A3784 G:A1309, G:A1311, G:A1310 2qao B3301 3Bout B3865, B3866, B3867, B3868, B3869, B3870 A:B42, G:B43, U:B434 2qbc B3301 3Bout B3865, B3866, B3867, B3868, B3869, B3870 G:B43, U:B434, A:B42 3df4 B3301 3Bout B4302, B4303, B4304, B4305, B4306, B4307 A:B42, G:B43, U:B434 2qao B3279 3Bout B3847, B3848, B3849, B3850, B3851, B3852 G:B2549, G:B2550, G:B2557 3df4 B3279 3Bout B4280, B4281, B4282, B4283, B4284, B4285 G:B2549, G:B2550, G:B2557 3df2 B3240 3Bout B4241, B4242, B4243, B4244, B4245 G:B2303, U:B2302, G:B2304 2qam B3240 3Bout B3805, B3806, B3807, B3808, B3809 G:B2304, U:B2302, G:B2303 4nvu A3155 3Bout A4032, A4033, A4034, A4035 G:A44, U:A45, G:A396 4nvy A3155 3Bout A4033, A4034, A4035, P101 G:A44, U:A45, G:A396 4qcy A3147 3Bout A4041, A4042, A4043, A4044, A4045 G:A44, G:A396, C:A43 4qd0 A3137 3Bout A4093, A4094, A4095, A4096, A4097 A:A684, G:A682, G:A683 4tpf A3132 3Bout A3781, A3782, A3783, A3784, C307, C308 U:A1825, C:A1793, G:A1826 4tox A3132 3Bout A3782, A3783, A3784, A3785, A3786, C307 C:A1793, U:A1825, G:A1826 4too A3132 3Bout A3777, A3778, A3779, A3780, A3781, A3782 U:A1825, G:A1826, U:A1827 4tp7 A3132 3Bout A3778, A3779, A3780, A3781, C310, C311 U:A1825, C:A1793, G:A1826

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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