MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·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 8 of 14 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v26 A1735 Pout·3Bout A2058, A2059, A2060, A2061, A2062, A2063 G:A394 G:A44, U:A45, C:A395 3v27 A3650 Pout·3Bout A5337, A5338, A5339, A5340, A5341, A5342 A:A2765 G:A2766, G:A2736, G:A2737 3v27 B220 Pout·3Bout A4908, B339, B340, B341, B342, B343 C:A951 G:B85, G:B86, C:B92 3v27 A3617 Pout·3Bout A5159, A5160, A5161, A5162, A5163, A5164 G:A686 G:A771, A:A689, G:A690 3v27 A3355 Pout·3Bout A4050, A4051, A4052, A4053, A4054, 7103 A:A1308 G:A1311, G:A1309, G:A1310 3v27 A3565 Pout·3Bout A4944, A4945, A4946, A4947, A4948, A4949 A:A835 A:A835, G:A942, U:A943 3v27 A3611 Pout·3Bout A5123, A5124, A5125, A5126, A5127, A5128 G:A1855 G:A1856, G:A1857, G:A1855 3v27 A3647 Pout·3Bout A5319, A5320, A5321, A5322, A5323, A5324 G:A11 U:A12, G:A10, G:A11 3v27 A3448 Pout·3Bout A3968, A4420, A4421, A4422, A4423, A4424 A:A103 G:A82, G:A80, G:A81 3v27 A3626 Pout·3Bout A5213, A5214, A5215, A5216, A5217 U:A1267 G:A2010, U:A2011, G:A2009 3v28 A1714 Pout·3Bout A1889, A1890, A1891, A1892, A1893 A:A119 U:A287, G:A285, G:A286 3v29 A3538 Pout·3Bout A4541, A4542, A4543, A4544, A4545, A4546 G:A2193 G:A2193, G:A2194, C:A2095 3v29 A3404 Pout·3Bout A4037, A4038, A4039, A4040, A4041, A4042 A:A103 G:A80, G:A82, G:A81 3v29 A3501 Pout·3Bout A4396, A4397, A4398, A4399 A:A1701 G:A1699, G:A1702, G:A1703 3v2c A1802 Pout·3Bout A2306, A2307, A2308, A2309, A2310 A:A781 G:A799, G:A798, G:A800 3v2d A3692 Pout·3Bout A5657, A5658, A5659, A5660, A5661, A5662 U:A1267 G:A2010, U:A2011, G:A2009 3v2d A3675 Pout·3Bout A5590, A5591, A5592, A5593, A5594 G:A2845 G:A2845, G:A2846, G:A2848 3v2d A3633 Pout·3Bout A5463, A5464, A5465, A5466, A5467 A:A2765 G:A2735, G:A2736, G:A2737 3v2f A3603 Pout·3Bout A5085, A5086, A5087, A5088, A5089 C:A1398 G:A1400, G:A1385, G:A1401 3v2f A3345 Pout·3Bout A4402, A4403, A4404, A4405, A4406 A:A2360 C:A2356, U:A2357, A:A2361 3v2f A3367 Pout·3Bout A4472, A4473, A4474, A4475, A4476 A:A1308 G:A1309, G:A1310, G:A1311 3v2f A3600 Pout·3Bout A5071, A5072, A5073, A5074, A5075, A5076 U:A1267 G:A2010, G:A2009, U:A2011 3v2f A3612 Pout·3Bout A5117, A5118, A5119, A5120, A5121 G:A2845 G:A2848, G:A2845, G:A2846 4a17 0204 Pout·3Bout 07059, 07060, 07061, 07062, 07063, 07064 A:374 U:376, A:3101, A:3100 4a1a 079 Pout·3Bout 05603, 05604, 05605, 05606, 05607, 05608 A:23 A:24, A:25, A:26

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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