MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbg:B2930, See in JSmolClick on the image to toggle views Site type: Pout·4Bout Schematic drawing for Pout·4Bout List of all 135 Mg2+ binding sites with the site type Pout·4Bout 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 4dr5 A1696 Pout·4Bout A2130, A2131, A2132, A2133 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4dr5 A1817 Pout·4Bout A2292, A2293, A2294, A2295, A2296, A2297 G:A1057 G:A1058, U:A1199, C:A1059, G:A1198 4dr6 A1705 Pout·4Bout A2256, A2257, A2258, N201 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4duy A1634 Pout·4Bout A1971, A1972, A1973, A1974, A1975 A:A583 G:A584, G:A585, C:A756, U:A757 4duz A1827 Pout·4Bout A2188, A2189, A2190, A2191, A2192 A:A766 U:A813, C:A812, A:A768, C:A811 4dv0 A1684 Pout·4Bout A2048, A2049, A2050, A2051 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4dv1 A1810 Pout·4Bout A2206, A2207, A2208, A2209, A2210, A2211 A:A766 U:A813, C:A811, C:A812, A:A767 4dv3 A1835 Pout·4Bout A2191, A2192, A2193, A2194, A2195, A2196 A:A766 A:A767, C:A812, A:A768, C:A811 4dv3 A1852 Pout·4Bout A2235, A2236, A2237, A2238, A2239 G:A266 G:A257, G:A266, U:A256, A:A270 4dv5 A1829 Pout·4Bout A2188, A2189, A2190, A2191, A2192, A2193 A:A766 C:A812, U:A813, A:A767, C:A811 4dv6 A1636 Pout·4Bout A1968, A1969, A1970, A1971, A1972 A:A583 G:A755, G:A584, G:A585, C:A756 4dv7 A1846 Pout·4Bout A2201, A2202, A2203, A2204, A2205, A2206 A:A766 U:A813, C:A812, A:A767, C:A811 4gaq A1620 Pout·4Bout A1790, A1791, A1792, A1793, A1794, A1795 U:A644 G:A645, G:A646, U:A593, U:A644 4gaq A1606 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267 4gd1 A1616 Pout·4Bout A1777, A1778, A1779, A1780, N201, N202 A:A1360 C:A980, A:A1360, G:A1361, C:A979 4gd1 A1610 Pout·4Bout A1745, A1746, A1747, A1748, A1749, A1750 U:A644 G:A646, C:A647, U:A593, G:A645 4gd2 A1623 Pout·4Bout A1809, A1810, A1811, A1812, A1813, A1814 A:A781 C:A797, U:A798, G:A800, G:A799 4gd2 A1612 Pout·4Bout A1754, A1755, A1756, A1757, A1758, A1759 A:A415 G:A416, G:A417, G:A425, U:A426 4ji0 A1701 Pout·4Bout A2066, A2067, A2068, A2069 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4ji1 A1655 Pout·4Bout A1988, A1989, A1990, A1991 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4ji6 A1839 Pout·4Bout A2330, A2658, A2659, A2660, A2661, A2662 G:A1057 C:A1059, G:A1198, G:A1058, U:A1199 4ji7 A1683 Pout·4Bout A2235, A2236, A2237, N201 A:A1360 C:A980, C:A979, G:A1361, A:A1360 4ji8 A1872 Pout·4Bout A2754, A2755, A2756, A2757, A2758, A2759 G:A1057 C:A1059, G:A1198, U:A1199, G:A1058 4kix A3002 Pout·4Bout A3207, A3209, A3210, A3211, A3212 A:A28 U:A29, G:A473, G:A474, G:A30 4nvv A3420 Pout·4Bout A4374, A4375, A4376, A4377 A:A28 G:A499, G:A500, U:A29, G:A30

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>