MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4k:A1546, See in JSmolClick on the image to toggle views Site type: Pout·2Bout Schematic drawing for Pout·2Bout List of all 343 Mg2+ binding sites with the site type Pout·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 11 of 14 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4gaq A1607 Pout·2Bout A1724, A1725, A1726, A1727, A1728, T101 G:A259 G:A260, G:A259 4gaq A1635 Pout·2Bout A1866, A1867, A1868, A1869, A1870, A1871 G:A1385 G:A1386, G:A1385 4gaq A1622 Pout·2Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803 G:A771, U:A772 4gar A3068 Pout·2Bout A3521, A3522, A3523, A3524, A3525 U:A2302 G:A2303, G:A2304 4gar A3113 Pout·2Bout A3716, A3717, A3718, T203 A:A1342 G:A1601, U:A1602 4gar A3082 Pout·2Bout A3582, A3583, A3584, A3585, A3586, A3587 A:A933 G:A841, U:A842 4gar A3015 Pout·2Bout A3278, A3279, A3280, A3281, A3282, A3283 G:A1256 U:A580, G:A1259 4gar A3131 Pout·2Bout A3794, A3795, A3796, A3797, A3798, 4201 A:A2741 C:A2755, G:A2742 4gau A3099 Pout·2Bout A3676, A3677, A3678, A3679, A3680, A3681 U:A2615 G:A2048, G:A2049 4gd1 A1602 Pout·2Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A315 G:A318, G:A319 4gd2 A1606 Pout·2Bout A1724, A1725, A1726, A1727, A1728, A1729 G:A259 G:A259, G:A260 4ji0 A1815 Pout·2Bout A2131, A2132, A2133, A2134, A2135, A2136 C:A398 C:A36, U:A37 4ji0 A1639 Pout·2Bout A1971, A1972, A1973, A1974, A1975 A:A583 G:A584, G:A585 4ji1 A1731 Pout·2Bout A2076, A2077, A2078, A2079, A2080, A2081 A:A753 G:A650, G:A649 4ji3 A1698 Pout·2Bout A2065, A2066, A2067, N201 A:A1360 C:A980, A:A1360 4ji4 A1638 Pout·2Bout A1968, A1969, A1970, A1971, Q301 A:A583 G:A584, G:A585 4ji5 A1723 Pout·2Bout A2054, A2055, A2056, A2057, A2058, A2059 A:A781 G:A799, G:A800 4ji5 A1694 Pout·2Bout A1893, A1894, A1895, A1896, A1897, A1898 U:A871 G:A853, G:A854 4ji6 A1778 Pout·2Bout A2301, A2302, A2303, A2304, A2305, A2306 A:A753 G:A649, G:A650 4ji6 A1930 Pout·2Bout A3175, A3176, A3177, A3178, A3179, A3180 A:A781 G:A798, G:A800 4ji6 A1762 Pout·2Bout A2205, A2206, A2207, A2208, A2209, A2210 U:A871 G:A854, G:A853 4ji7 A1994 Pout·2Bout A3469, A3470, A3471, A3472, A3473, A3474 U:A646 C:A586, G:A587 4ji7 A1800 Pout·2Bout A2311, A2312, A2313, A2314, A2315, A2316 U:A871 G:A853, G:A854 4ji7 A1631 Pout·2Bout A2158, A2159, A2160, A2161, A2162 A:A583 G:A584, G:A585 4nvu A3165 Pout·2Bout A4048, A4049, A4050, A4051 G:A803 G:A771, U:A772

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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