MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 199 Mg2+ binding sites with the site type 2Pout·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 7 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4gas A1622 2Pout·3Bout A1802, A1803, A1804, A1805, A1806, A1807 G:A803, U:A804 G:A771, U:A772, G:A773 4gau A3089 2Pout·3Bout A3626, A3627, A3628, A3629, A3630, A3631 G:A1422, A:A1572 G:A1423, G:A1425, G:A1424 4gau A3081 2Pout·3Bout A3588, A3589, A3590, A3591, A3592, A3593 G:A976, G:A977 G:A978, A:A979, G:A977 4gd2 A1608 2Pout·3Bout A1734, A1735, A1736, A1737, A1738, A1739 A:A315, A:A329 G:A319, A:A320, G:A318 4gd2 A1622 2Pout·3Bout A1803, A1804, A1805, A1806, A1807, A1808 G:A803, U:A804 G:A771, U:A772, G:A773 4ji1 A1788 2Pout·3Bout A2420, A2421, A2422, A2423, A2424, A2425 G:A266, G:A265 G:A257, G:A258, G:A259 4ji5 A1700 2Pout·3Bout A1929, A1930, A1931, A1932, A1933, A1934 U:A804, G:A803 G:A771, U:A772, C:A770 4ji6 A1803 2Pout·3Bout A2445, A2446, A2447, A2448, A2449, A2450 U:A804, G:A803 G:A771, U:A772, C:A770 4ji7 A1850 2Pout·3Bout A2617, A2618, A2619, A2620, A2621, A2622 U:A804, G:A803 G:A771, U:A772, C:A770 4ji8 A1832 2Pout·3Bout A2514, A2515, A2516, A2517, A2518, A2519 U:A804, G:A803 G:A771, U:A772, C:A770 4nvy A3145 2Pout·3Bout A4011, A4012, A4013, A4014 U:A582, A:A583 G:A585, G:A584, U:A757 4pea A1606 2Pout·3Bout A1724, A1725, A1726, A1727, T101, T102 G:A258, G:A259 G:A258, G:A259, G:A260 4pea A1622 2Pout·3Bout A1799, A1800, A1801, A1802, A1803, A1804 G:A803, U:A804 G:A771, U:A772, G:A773 4pec A3081 2Pout·3Bout A3568, A3569, A3570, A3571, A3572, 0101 C:A2055, A:A574 U:A2034, G:A2035, A:A574 4pec A3018 2Pout·3Bout A3285, A3286, A3287, A3288, A3289, E304 A:A608, A:A616 G:A617, G:A619, G:A618 4qcn A3308 2Pout·3Bout A4116, A4117, A4118, A4119, A4120, A4121 A:A323, C:A360 A:A324, A:A323, G:A362 4qcq A3170 2Pout·3Bout A4157, A4158, A4159, V102, V103 G:A1401, G:V18 G:A1401, C:A1399, G:V18 4qcr A3718 2Pout·3Bout A5193, A5194, A5195, A5196, A5197 G:A733, C:A734 U:A735, G:A818, G:A737 4qcr A3327 2Pout·3Bout A4130, A4131, A4132, A4133, A4134, A4135 A:A323, C:A360 A:A324, A:A323, G:A362 4qct A3268 2Pout·3Bout A4067, A4068, A4069, A4070, A4071, A4072 A:A299, C:A336 A:A300, A:A299, G:A338 4qcv A3296 2Pout·3Bout A4124, A4125, A4126, A4127, A4128, A4129 A:A323, C:A360 A:A324, A:A323, G:A362 4qcz A3309 2Pout·3Bout A4117, A4118, A4119, A4120, A4121, A4122 A:A323, C:A360 A:A324, A:A323, G:A362 4qd1 A3517 2Pout·3Bout A4527, A4528, A4529, A4530, A4531, A4532 A:A2435, A:A2434 U:A2431, U:A827, A:A2426 4qd1 A3296 2Pout·3Bout A4060, A4061, A4062, A4063, A4064, A4065 A:A299, C:A336 A:A300, G:A338, A:A299 4tol A1602 2Pout·3Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A329, A:A315 A:A320, G:A318, 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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