MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·3Bout 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 14 | « 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 1egk C9 Pout·3Bout B64, C64, C65, C67, C68, D63 G:C103 DG:B36, DA:B45, DG:D132 1egk A25 Pout·3Bout A46, A47, A48, B65, B66, D70 G:A3 DG:B32, DG:D136, DA:D135 1ffy T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55 1hr2 A16 Pout·3Bout A353, A354, A355, A356, A357, A358 A:A114 G:A116, U:A205, A:A115 1qu2 T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55 1vs5 A1563 Pout·3Bout A1696, A1697, A1698, A1699, A1700, A1701 G:A266 G:A257, G:A258, G:A259 1vs5 A1558 Pout·3Bout A1672, A1673, A1674, A1675, N142, N143 A:A1360 C:A980, G:A1361, A:A1360 1vs7 A1568 Pout·3Bout A1724, A1725, A1726, A1727, A1728, A1729 A:A781 U:A798, G:A800, G:A799 1vs7 A1567 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 1vs7 A1559 Pout·3Bout A1677, A1678, A1679, A1680, N150 A:A1360 C:A980, G:A1361, A:A1360 1vs8 B2956 Pout·3Bout B3263, B3264, B3265, B3266, B3267, B3268 A:B2386 C:B2326, U:B2387, A:B2386 1vt2 A2992 Pout·3Bout A3457, A3458, A3459, A3460, A3461, A3462 G:A977 G:A977, G:A978, G:A976 1vt2 A3015 Pout·3Bout A3547, A3548, A3549, A3550, A3551, 2647 U:A686 G:A771, U:A769, G:A770 1yj9 08071 Pout·3Bout 03935, 05862, 07216, 07347, 07618 A:01815 U:01813, C:01818, U:01817 2avy A1557 Pout·3Bout A1671, A1672, N130, N131, N132, N135 A:A1360 C:A980, G:A1361, A:A1360 2avy A1563 Pout·3Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A781 G:A799, G:A800, U:A798 2aw4 B2922 Pout·3Bout B3095, B3096, B3097, B3098, B3099, B3100 U:B1267 G:B2010, U:B2011, G:B2012 2aw7 A1558 Pout·3Bout A1678, A1679, A1680, A1681, N141 A:A1360 C:A980, A:A1360, G:A1361 2aw7 A1567 Pout·3Bout A1725, A1726, A1727, A1728, A1729, A1730 A:A781 G:A800, U:A798, G:A799 2aw7 A1566 Pout·3Bout A1719, A1720, A1721, A1722, A1723, A1724 G:A266 G:A257, G:A258, G:A259 2awb B2957 Pout·3Bout B3267, B3268, B3269, B3270, B3271, B3272 A:B2386 C:B2326, U:B2387, A:B2386 2gcs B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101 2h0x B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101 2i2p A1563 Pout·3Bout A1703, A1704, A1705, A1706, K165, K168 A:A781 G:A799, G:A800, U:A798 2i2p A1575 Pout·3Bout A1765, A1766, A1767, A1768, A1769 U:A1348 G:A1370, G:A1371, U:A1372

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>