MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 6 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4gau A3132 2Pout·Bout A3808, A3809, A3810, A3811, A3812, A3813 G:A2004, A:A1650 G:A1651 4gau A3087 2Pout·Bout A3616, A3617, A3618, A3619 A:A1359, G:A1360 G:A1361 4ji0 A1608 2Pout·Bout A1913, A1914, A1915, A1916 U:A751, U:A652 G:A752 4ji1 A1751 2Pout·Bout A2195, A2196, A2197, A2198, A2199, A2200 G:A361, G:A362 G:A362 4ji1 A1758 2Pout·Bout A2237, A2238, A2239, A2240, A2241, A2242 C:A307, C:A308 G:A309 4ji1 A1766 2Pout·Bout A2284, A2285, A2286, A2287, A2288, A2289 A:A1394, A:A918 A:A919 4ji5 A1606 2Pout·Bout A1816, A1817, A1818, A1819, A1820 C:A620, A:A621 G:A617 4ji6 A1904 2Pout·Bout A3041, A3042, A3043, A3044, A3045, A3046 A:A151, G:A168 G:A168 4ji7 A1609 2Pout·Bout A2119, A2120, A2121, A2122, A2123 C:A620, A:A621 G:A617 4ji7 A1638 2Pout·Bout A2172, A2173, A2174, A2175 C:A754, U:A646 G:A587 4ji7 A1956 2Pout·Bout A3241, A3242, A3243, A3244, A3245, A3246 A:A53, A:A353 A:A353 4ji8 A1609 2Pout·Bout A2019, A2020, A2021, A2022, A2023 C:A620, A:A621 G:A617 4nvx A3444 2Pout·Bout A4495, A4496, A4497, A4498 G:A1904, G:A2597 G:A2595 4nvz A3608 2Pout·Bout A4871, A4872, A4873, A4874 G:A2609, G:A1926 G:A2607 4nw0 A3090 2Pout·Bout A4038, A4039, A4040, A4041 U:A804, G:A803 G:A771 4nw1 A3415 2Pout·Bout A4449, A4450, A4451, 7102 G:A770, G:A686 G:A770 4nw1 A3438 2Pout·Bout A4494, A4495, A4496, A4497 G:A1904, G:A2597 G:A2595 4peb A3133 2Pout·Bout A3796, A3797, A3798, A3799, 4201, 4202 A:A2741, A:A2740 G:A2742 4pec A3133 2Pout·Bout A3789, A3790, A3791, A3792, A3793, 4201 A:A2741, A:A2740 G:A2742 4qcn A3591 2Pout·Bout A4968, A4969, A4970, A4971, A4972, A4973 G:A2609, G:A1926 G:A2607 4qcn A3580 2Pout·Bout A4938, A4939, A4940, A4941, A4942 U:A2792, G:A2793 A:A553 4qcn A3496 2Pout·Bout A4662, A4663, A4664, A4665, A4666 A:A1399, A:A1400 G:A1402 4qcn A3479 2Pout·Bout A4616, A4617, A4618, A4619 A:A2788, C:A2787 A:A2788 4qcp A3473 2Pout·Bout A4601, A4602, A4603, A4604, A4605 G:A2597, G:A1904 G:A2595 4qcp A3452 2Pout·Bout A4552, A4553, A4554, A4555 G:A770, G:A771 G:A770

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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