MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 174 Mg2+ binding sites with the site type 4Pout 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 1ehz A560 4Pout A725, A726, A727, A728, A729, A730 U:A12, U:A8, A:A9, C:A11 1ffy T1201 4Pout T1292, T1293, T1294, T1295, T1296, T1297 U:T54, U:T55, A:T57, C:T56 1qu2 T1201 4Pout T1292, T1293, T1294, T1295, T1296, T1297 U:T54, U:T55, A:T57, C:T56 1vs5 A1560 4Pout A1680, A1681, A1682, A1683, A1684, A1685 A:A16, G:A15, U:A13, U:A14 1vs5 A1556 4Pout A1661, A1662, A1663, A1664, A1665, N130 A:A1204, G:A1048, U:A1049, C:A1203 1vs7 A1551 4Pout A1638, A1639, A1640, A1641, A1642, A1643 G:A350, C:A334, U:A333, A:A349 1vs7 A1549 4Pout A1629, A1630, A1631, A1632, A1633, A1634 A:A16, U:A13, U:A14, G:A15 1vs7 A1557 4Pout A1667, A1668, A1669, A1670, N135, N138 C:A1203, A:A1204, U:A1049, G:A1048 1yls D247 4Pout B384, B385, B386, B387, B388, D383 C:B235, G:D236, G:B236, C:D235 2avy A1559 4Pout A1677, A1678, A1679, A1680, A1681, A1682 A:A16, G:A15, U:A13, U:A14 2aw7 A1550 4Pout A1638, A1639, A1640, A1641, A1642, A1643 G:A350, C:A334, U:A333, A:A349 2aw7 A1556 4Pout A1667, A1668, A1669, A1670, A1671, N129 G:A1048, C:A1203, A:A1204, U:A1049 2aw7 A1548 4Pout A1628, A1629, A1630, A1631, A1632, A1633 A:A16, U:A13, U:A14, G:A15 2i2t B3004 4Pout B3475, B3476, B3477, B3478, B3479, B3480 U:B202, C:B383, C:B385, G:B205 2i2t B3022 4Pout B3550, B3551, B3552, B3553, B3554, N773 C:B2874, G:B2819, G:B2838, A:B2820 2i2t B2908 4Pout B3040, B3041, B3042, B3043, B3044, B3045 G:B559, C:B560, G:B2038, A:B1008 2i2v B3023 4Pout B3551, B3552, B3553, B3554, B3555, N1073 C:B2874, G:B2819, G:B2838, A:B2820 2i2v B2967 4Pout B3325, B3326, B3327, B3328, B3329, B3330 C:B560, G:B2038, G:B559, A:B1008 2otl 08072 4Pout 03241, 04009, 07413, 07817, 07874 U:0954, C:02298, G:02299, A:02301 2qal A2096 4Pout A2097, A2098, A2099, A2100, A2101, A2102 U:A13, U:A14, G:A15, A:A16 2qam B3382 4Pout B3923, B3924, B3925, B3926, B3927, B3928 A:B1669, C:B1986, A:B1987, C:B2551 2qan A2077 4Pout A2079, A2080, A2082, A2083, N2078, N2081 C:A1203, A:A1204, G:A1048, U:A1049 2qan A2029 4Pout A2030, A2031, A2032, A2033, A2034, A2035 A:A16, U:A14, U:A13, G:A15 2qan A2042 4Pout A2043, A2044, A2045, A2046, A2047, A2048 G:A350, C:A334, U:A333, A:A349 2qao B3344 4Pout B3901, B3902, B3903, B3904, B3905, B3906 U:B1915, A:B1912, A:B1913, A:B1916

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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