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 1 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 1egk A24 2Pout·Bout A40, A41, A42, A43, A44, A45 A:A19, DC:D153 A:A19 1vs5 A1566 2Pout·Bout A1711, A1712, A1713, A1714, A1715, A1716 A:A729, G:A727 G:A727 1vs7 A1570 2Pout·Bout A1734, A1735, A1736, A1737, A1738, A1739 C:A726, G:A727 G:A727 1vs8 N128 2Pout·Bout B3286, B3287, B3288, N391, N394, N396 G:B1653, A:B2820 G:B2822 2avy A1550 2Pout·Bout A1638, A1639, A1640, A1641, A1642, A1643 A:A329, A:A315 G:A319 2aw4 B2997 2Pout·Bout B3434, B3435, B3436, B3437, B3438, B3439 U:B686, C:B687 G:B770 2awb N128 2Pout·Bout B3289, B3290, B3291, N391, N394, N396 G:B1653, A:B2820 G:B2822 2awb B2959 2Pout·Bout B3277, B3278, B3279, B3280, B3281, Q381 A:B582, A:B1253 C:B584 2i2u A1586 2Pout·Bout A1811, A1812, A1813, A1814, A1815, A1816 G:A1356, A:A1357 C:A1359 2i2u A1582 2Pout·Bout A1788, A1789, A1790, A1791, A1792, A1793 A:A1046, G:A1047 G:A1047 2qal A2328 2Pout·Bout A2329, A2330, A2331, A2332, A2333, A2334 A:A1394, A:A918 A:A919 2qal A2231 2Pout·Bout A2232, A2234, A2235, A2236, T2233 U:A323, G:A324 G:A324 2qal A2143 2Pout·Bout A2144, A2145, A2146, A2147, A2148, A2149 A:A1357, G:A1356 C:A1359 2qao B3337 2Pout·Bout B3895, B3896, B3897, B3898, B3899, B3900 G:B1653, G:B2819 A:B2821 2qb9 A2007 2Pout·Bout A2364, A2365, A2366, A2367, A2368, A2369 G:A1079, G:A1077 G:A1077 2qb9 A2143 2Pout·Bout A2472, A2473, A2474, A2475, A2476, A2477 A:A1357, G:A1356 C:A1359 2qba B3521 2Pout·Bout B4032, B4033, B4034, B4035, B4036, B4037 U:B769, G:B770 G:B770 2qbb A2353 2Pout·Bout A2659, A2660, A2661, A2662, A2663, A2664 G:A259, G:A258 G:A259 2qbb A2049 2Pout·Bout A2410, A2411, A2412, A2413, A2414, A2415 A:A171, A:A172 G:A148 2qbf E167 2Pout·Bout A1728, A1729, A1730, A1731, A1732 U:A20, G:A21 G:A21 2qbf A1601 2Pout·Bout T358, A1892, A1893, A1894, A1895, A1896 G:A259, G:A258 G:A259 2qbh A1566 2Pout·Bout A1713, A1714, A1715, A1716, A1717, A1718 A:A1357, G:A1356 C:A1359 2qbi B2997 2Pout·Bout B3433, B3434, B3435, B3436, B3437, B3438 U:B769, G:B770 G:B770 2qbj A1551 2Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A171, A:A172 G:A148 2qou A1550 2Pout·Bout A1933, A1934, A1935, A1936, A1937, A1938 C:A316, A:A315 G:A319

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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