MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·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 5 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 3ora A1552 Pout·Bout A1665, A1666, A1667, A1668, A1669, A1670 G:A1079 G:A1077 3r1l C1033 Pout·Bout C1063, C1064, C1065, C1066, C1067, C1068 U:C49 C:C70 3r8s A2973 Pout·Bout A3420, A3421, A3422, A3423, A3424 C:A2310 G:A2304 3v22 A1684 Pout·Bout A1851, A1852, A1853, A1854, A1855 G:A1079 G:A1077 3v23 A3613 Pout·Bout A5071, A5072, A5073, A5074, A5075, A5076 A:A1809 G:A1807 3v23 A3350 Pout·Bout A4074, A4075, A4076, A4077, A4078 C:A1004 G:A1136 3v23 A3615 Pout·Bout A5082, A5083, A5084, A5085, A5086, A5087 A:A2377 G:A2375 3v25 A3418 Pout·Bout A4142, A4143, A4144, A4145, A4146 U:A1397 G:A1400 3v26 A1730 Pout·Bout A2029, A2030, A2031, A2032, A2033, A2034 G:A803 G:A771 3v26 A1694 Pout·Bout A1872, A1873, A1874, A1875, A1876 G:A724 G:A724 3v27 A3616 Pout·Bout A5153, A5154, A5155, A5156, A5157, A5158 G:A465 G:A463 3v27 A3531 Pout·Bout A4785, A4786, A4787, A4788, A4789, A4790 A:A1809 G:A1807 3v27 A3507 Pout·Bout A4672, A4673, A4674, A4675, A4676 U:A1357 G:A1371 3v27 A3641 Pout·Bout A5289, A5290, A5291, A5292, P309, P310 G:A1193 A:A1194 3v27 A3615 Pout·Bout A5147, A5148, A5149, A5150, A5151, A5152 G:A1283 G:A1283 3v27 A3603 Pout·Bout A5084, A5085, A5086, A5087, A5088, A5089 C:A2774 A:A2775 3v27 A3624 Pout·Bout A5201, A5202, A5203, A5204, A5205, A5206 G:A765 G:A765 3v27 A3522 Pout·Bout A4739, A4740, A4741, A4742, A4743 A:A983 A:A572 3v29 A3589 Pout·Bout A4728, A4729, A4730, A4731, A4732, A4733 U:A2615 G:A2049 3v2d A3724 Pout·Bout A5767, A5768, A5769, A5770, A5771, A5772 G:A2859 G:A2857 3v2d A3681 Pout·Bout A5611, A5612, A5613, A5614, A5615 G:A465 G:A463 3v2d A3715 Pout·Bout A5739, A5740, A5741, 8208, 8209 A:A632 G:A630 3v2d A3395 Pout·Bout A4812, A4813, A4814, A4815, A4816 A:A332 A:A331 3v2d A3571 Pout·Bout A5324, A5325, A5326, A5327 U:A606 G:A620 3v2d A3706 Pout·Bout A5711, A5712, A5713, A5714, A5715, A5716 A:A1809 G:A1807

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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