MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 131 Mg2+ binding sites with the site type 3Pout·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 4 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v29 A3382 3Pout·2Bout A3940, A3941, A3942, A3943, A3944, A3945 A:A1634, U:A1300, G:A1627 G:A1628, U:A1629 3v29 A3374 3Pout·2Bout A3908, A3909, A3910, A3911, A3912, P303 G:A831, G:A944, U:A568 A:A2448, A:A945 3v2c A1673 3Pout·2Bout A2018, A2019, A2020, A2021, A2022 A:A780, G:A799, C:A779 G:A800, A:A780 3v2d A3363 3Pout·2Bout A4701, A4702, A4703, A4704, A4705, A4706 G:A1332, C:A1333, U:A1313 U:A1335, G:A1334 3v2f A3319 3Pout·2Bout A4318, A4319, A4320, A4321, A4322 G:A1358, U:A1357, C:A1370 G:A1371, G:A1358 4bpp A5069 3Pout·2Bout A8115, A8116, A8117, A8118, A8119, A8120 C:A1428, C:A1149, G:A1148 A:A1174, G:A1172 4dha A3731 3Pout·2Bout A4833, A4834, A4835, A4836, A4837, A4838 G:A770, G:A686, G:A771 G:A771, G:A770 4dr4 A1948 3Pout·2Bout A2434, A2435, A2436, A2437, A2438 A:A608, A:A609, A:A607 A:A609, G:A610 4duz A1840 3Pout·2Bout A2218, A2219, A2220, A2221, A2222 G:A858, C:A868, C:A857 G:A858, G:A869 4duz A1839 3Pout·2Bout A2212, A2213, A2214, A2215, A2216, A2217 G:A581, U:A757, U:A580 G:A758, G:A581 4dv0 A1799 3Pout·2Bout A2174, A2175, A2176, A2177, A2178, A2179 C:A857, C:A868, G:A869 G:A858, G:A869 4dv0 A1788 3Pout·2Bout A2139, A2140, A2141, A2142 C:A307, C:A308, G:A306 G:A309, G:A310 4dv1 A1821 3Pout·2Bout A2238, A2239, A2240, A2241, A2242, A2243 C:A868, G:A869, C:A857 G:A858, G:A869 4dv1 A1820 3Pout·2Bout A2232, A2233, A2234, A2235, A2236, A2237 U:A757, U:A580, G:A758 G:A581, G:A758 4dv3 A1848 3Pout·2Bout A2215, A2216, A2217, A2218, A2219, A2220 U:A757, G:A581, U:A580 G:A581, G:A758 4dv4 A1800 3Pout·2Bout A2163, A2164, A2165, A2166, A2167, A2168 C:A868, G:A869, C:A857 G:A858, G:A869 4dv6 A1824 3Pout·2Bout A2237, A2238, A2239, A2240, A2241, A2242 G:A858, C:A868, G:A869 G:A858, G:A869 4dv7 A1863 3Pout·2Bout A2234, A2235, A2236, A2237, A2238, A2239 G:A858, C:A868, C:A857 G:A858, G:A869 4dv7 A1862 3Pout·2Bout A2228, A2229, A2230, A2231, A2232, A2233 G:A581, U:A580, G:A758 G:A758, G:A581 4gaq D301 3Pout·2Bout A1774, A1775, A1776, D401, D402 ARG:D70(NH1) C:A401, A:A547, G:A548 G:A402, C:A401 4gau A3059 3Pout·2Bout A3481, A3482, A3483, A3484, A3485, A3486 G:A2578, U:A2613, A:A2051 A:A2051, A:A2614 4gau A3042 3Pout·2Bout A3401, A3402, A3403, A3404 G:A1358, C:A1357, C:A1370 G:A1358, G:A1371 4ji2 A1613 3Pout·2Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617, G:A616 4ji5 A1718 3Pout·2Bout A2033, A2034, A2035, A2036, A2037, A2038 G:A869, G:A858, C:A868 G:A858, G:A869 4ji6 A1607 3Pout·2Bout A2020, A2021, A2022, A2023, A2024 G:A617, A:A621, C:A620 G:A616, G:A617

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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