MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3v2d 3V2D (2.7Å) -- RIBOSOME : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu List of all 177 Mg2+ binding sites in the PDB structure 3v2d in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 6 of 9 | « 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 3v2d A3401 trans-2Oph A:A751(OP1), A:A1614(OP1) A4834, A4835, A4836, A4837 G:A1613 A:A751, C:A1617, A:A789, A:A1614 3v2d A3224 trans-2Oph U:A2682(OP2), A:A2721(OP1) A4316, A4317, A4318, T301 C:A2683, G:A2722 3v2d A3137 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A4064, A4065 G:A194, A:A195 3v2d A3548 fac-3Oph A:A2711(OP2), A:A2712(OP2), G:A2714(OP2) A5258, A5259, A5260 C:A2710, A:A2713 3v2d A3314 fac-3Oph C:A2573(OP1), G:A2574(OP1), C:A2575(OP2) A4570, A4571, A4572 C:A2507 3v2d A3718 Bout A5747, A5748, A5749, A5750 G:A993 3v2d A3689 Bout A5642, A5643, A5644, A5645, A5646, A5647 G:A2000 3v2d A3558 Rout·Bout A5290, A5291, A5292, A5293 A:A282 A:A282 3v2d A3698 2Bout A5684, A5685, A5686, A5687, F416, F417 G:A798, G:A799 3v2d A3392 2Bout A4800, A4801, A4802, A4803, A4804 G:A2642, G:A2643 3v2d A3685 2Bout A5630, A5631, A5632, A5633, A5634 A:A2821, G:A2819 3v2d A3259 2Bout A4409, A4410, A4411, A4412, A4413 G:A1485, G:A1484 3v2d A3691 2Bout A5652, A5653, A5654, A5655, A5656 G:A2830, G:A2831 3v2d A3578 3Bout A5343, A5344, A5345, A5346 G:A407, G:A406, U:A421 3v2d A3167 Rout·3Bout A4157, A4158, A4159, A4160, A4161 U:A1142 G:A1015, G:A1016, G:A1017 3v2d A3373 4Bout A4736, A4737, A4738, A4739, A4740 U:A2457, G:A2494, G:A2495, G:A2455 3v2d A3372 4Bout A4731, A4732, A4733, A4734, A4735 G:A558, G:A559, G:A533, U:A534 3v2d A3308 6Bout A4548, A4549, A4550, A4551, A4552, A4553 A:A2241, U:A2074, U:A2243, G:A2238, G:A2242, U:A2075 3v2d A3266 Pout·Bout A4428, A4429, A4430, A4431, A4432, A4433 G:A1283 G:A1283 3v2d A3571 Pout·Bout A5324, A5325, A5326, A5327 U:A606 G:A620

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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