MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df4:B3602, See in JSmolClick on the image to toggle views Site type: Pout·Rout·2Bout Schematic drawing for Pout·Rout·2Bout List of all 40 Mg2+ binding sites with the site type Pout·Rout·2Bout 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 1 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1kqs 08076 Pout·Rout·2Bout 06351, 07324, 07325, 07377, 07378, 17875 U:01419 U:01418 G:01443, G:01444 1nji A8076 Pout·Rout·2Bout A6848, A7834, A7835, A7891, A7892, 37875 U:A1419 U:A1418 G:A1443, G:A1444 1n8r A8076 Pout·Rout·2Bout A7233, A8396, A8397, A8449, A8450, 37875 U:A1419 U:A1418 G:A1443, G:A1444 1m1k A8076 Pout·Rout·2Bout A6449, A7430, A7431, A7482, A7483, 37875 U:A1419 U:A1418 G:A1443, G:A1444 1jj2 08076 Pout·Rout·2Bout 06397, 07389, 07390, 07445, 07446, 17875 U:01419 U:01418 G:01443, G:01444 1m90 A8076 Pout·Rout·2Bout A6391, A7372, A7373, A7427, A7428, 37875 U:A1419 U:A1418 G:A1443, G:A1444 1kc8 A8076 Pout·Rout·2Bout A6849, A7841, A7842, A7895, A7896, 37875 U:A1419 U:A1418 G:A1443, G:A1444 3cxc 08076 Pout·Rout·2Bout 07749, 08734, 08735, 08787, 08788, 17875 U:01419 U:01418 G:01443, G:01444 1vq7 08076 Pout·Rout·2Bout 07100, 08154, 08155, 08207, 08208, 27875 U:01419 U:01418 G:01443, G:01444 1vq6 08076 Pout·Rout·2Bout 07065, 08123, 08124, 08173, 08174, 08175 U:01419 U:01418 G:01443, G:01444 1q82 A8076 Pout·Rout·2Bout A6336, A7314, A7366, A7367, 37875 U:A1419 U:A1418 G:A1444, G:A1443 4bpe A5078 Pout·Rout·2Bout A2391, A2392, A2398, A2399, A2400, A2470 U:A1277 G:A1276 G:A1296, A:A1297 4bpo A5078 Pout·Rout·2Bout A2251, A2254, A2258, A2259, A2260, A2467 U:A1277 G:A1276 G:A1296, A:A1297 4bpn A5072 Pout·Rout·2Bout A6570, A6571, A6572, A6573, A6574, A6576 U:A1467 C:A1466 A:A1457, U:A1492 4bpe A5056 Pout·Rout·2Bout A2003, A2209, A2210, A2331, A2332, A2333 G:A1113 U:A8 G:A1113, G:A1114 4bpo A5056 Pout·Rout·2Bout A2002, A2214, A2215, A2426, A2427, A2428 G:A1113 U:A8 G:A1113, G:A1114 3v2d A3664 Pout·Rout·2Bout A5557, A5558, A5559, A5560, A5561 A:A983 U:A562 A:A572, C:A975 4qct A3619 Pout·Rout·2Bout A4920, A4921, A4922, A4923, A4924, A4925 G:A396 U:A395 G:A397, G:A398 3v27 A3608 Pout·Rout·2Bout A5108, A5109, A5110, A5111, A5112, A5113 A:A1142 U:A1142 G:A1016, G:A1017 3df4 B3602 Pout·Rout·2Bout B4603, B4604, B4605, B4606, B4607, B4608 A:B973 A:B972 A:B820, A:B821 3v23 A3589 Pout·Rout·2Bout A4928, A4929, A4930, A4931, A4932, A4933 A:A1142 U:A1142 G:A1017, G:A1016 3v27 A3561 Pout·Rout·2Bout A4921, A4922, A4923, A4924, A4925, A4926 U:A504 A:A503 G:A498, A:A482 3v27 A3518 Pout·Rout·2Bout A4718, A4719, A4720, A4721, A4722, A4723 A:A1528 G:A1527 U:A1540, G:A1541 3v29 A3426 Pout·Rout·2Bout A4126, A4127, A4128, A4129 U:A2696 G:A1707 G:A1758, G:A1707 4qcr A3341 Pout·Rout·2Bout A4165, A4166, A4167, A4168 U:A2708 G:A1754 G:A1789, G:A1754

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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