MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 3 of 9 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tp2 A1631 3Pout A1846, A1847, A1848, A1849, A1850, A1851 U:A1049, A:A1204, G:A1048 4tow A1631 3Pout A1843, A1844, A1845, A1846, A1847, N203 U:A1049, A:A1204, G:A1048 4tp6 A1631 3Pout A1846, A1847, A1848, A1849, A1850, N202 G:A1048, U:A1049, A:A1204 4tpe A1631 3Pout A1846, A1847, A1848, A1849, A1850, N203 G:A1048, U:A1049, A:A1204 4pea A1631 3Pout A1843, A1844, A1845, A1846, A1847, N203 U:A1049, A:A1204, G:A1048 4ton A1631 3Pout A1844, A1845, A1846, A1847, A1848, N203 U:A1049, A:A1204, G:A1048 4tpa A1631 3Pout A1846, A1847, A1848, A1849, A1850, N202 U:A1049, A:A1204, G:A1048 4gas A1631 3Pout A1845, A1846, A1847, A1848, A1896, N204 U:A1049, A:A1204, G:A1048 4ji6 A1637 3Pout A2076, A2077, A2078, A2079 A:A16, U:A13, U:A14 4dv2 A1638 3Pout A1977, A1978, A1979, A1980 U:A820, C:A578, G:A576 4ji2 A1640 3Pout A1978, A1979, A1980, A1981 C:A578, G:A576, U:A820 4ji7 A1642 3Pout A2179, A2180, A2181, A2182 A:A16, U:A13, U:A14 4dr7 A1651 3Pout A2129, A2130, A2131, A2132 G:A15, A:A16, U:A13 4dr1 A1654 3Pout A2002, A2003, A2004, A2005 G:A15, A:A16, U:A13 4dr2 A1681 3Pout A2180, A2181, A2182, A2183 G:A15, A:A16, U:A13 3v22 A1698 3Pout A1910, A1911, A1912, A1913 C:A578, C:A817, G:A576 4dr7 A1715 3Pout A2282, A2283, A2284, A2285 A:A946, G:A945, G:A944 4ji1 A1746 3Pout A2165, A2166, A2167, A2168, A2169, A2170 G:A800, U:A801, G:A778 4ji1 A1757 3Pout A2231, A2232, A2233, A2234, A2235, A2236 G:A588, C:A589, G:A644 4dv7 A1785 3Pout A2100, A2101, A2102, A2103, A2104, A2105 C:A1103, A:A1101, C:A1100 4dv4 A1786 3Pout A2122, A2123, A2124, A2125 A:A151, C:A150, G:A168 3v2e A1798 3Pout A2289, A2290, A2291, A2292 G:A568, A:A864, U:A863 4dr5 A1814 3Pout A2274, A2275, A2276, A2277, A2278, A2279 C:A934, U:A1345, A:A1346 4lfb A1820 3Pout A1909, A1910, A1911, A1912, A1913, A1914 A:A16, G:A15, U:A14 4duy A1837 3Pout A2312, A2313, A2314, A2315, A2316, A2317 U:A1345, C:A934, A:A1346

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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