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 1 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 3v2f 8101 3Pout A4833, A4834, 6202, 6203, 8203 C:A2347, U:A2348, U:A2419 3v27 5103 3Pout 5201, 5202, 5203, 5204, 5205 G:A16, G:A518, G:A17 3owz B106 3Pout A139, A140, B117, B118, B119, B120 C:A66, A:A33, A:B33 3oww A107 3Pout A149, A150, A151, A152, A153, B134 G:A32, U:A67, G:B10 3oxj B108 3Pout A137, B126, B127, B128, B129, B130 G:A10, G:B32, U:B67 3og0 C272 3Pout A3161, A3162, A3163, A3164 G:A2599, G:A784, G:A2588 3ofd C272 3Pout A3163, A3164, C273, C274 G:A784, G:A2588, G:A2599 3oas C272 3Pout A3163, A3164, A3165, A3166 G:A2599, G:A784, G:A2588 3i22 C273 3Pout A3164, A3165, A3166, C275 G:A2599, G:A784, G:A2588 2i2u N340 3Pout A1783, A1784, A1785, A1786, A1787, N192 A:A1204, G:A1048, U:A1049 4jnx B501 3Pout A401, A402, B611, B612, B613, B614 U:B412, G:B413, C:B411 3td0 A1000 3Pout A1002, A1004, A1005, B1001, B1003, B1006 C:A12, C:B30, G:B31 3i21 A1547 3Pout A1652, A1653, A1654, A1655, A1656, N130 A:A1204, G:A1048, U:A1049 3i1s A1547 3Pout A1653, A1654, A1655, A1656, A1657, N130 A:A1204, G:A1048, U:A1049 2qow A1548 3Pout A1907, A1908, A1909, A1910, A1911, A1912 U:A14, A:A16, G:A15 2qp0 A1548 3Pout A1908, A1909, A1910, A1911, A1912, A1913 U:A14, U:A13, G:A15 2qbf A1548 3Pout A1627, A1628, A1629, A1630, A1631, A1632 G:A15, U:A13, U:A14 2z4m A1549 3Pout A1628, A1629, A1630, A1631, A1632, A1633 A:A16, U:A14, G:A15 3i1q A1550 3Pout A1653, A1654, A1655, A1656, N128, N132 C:A1203, A:A1204, G:A1048 2qbf A1550 3Pout A1638, A1639, A1640, A1641, A1642, A1643 U:A333, G:A350, C:A334 3ofp A1550 3Pout A1652, A1653, A1654, A1655, A1656, N105 A:A1204, G:A1048, U:A1049 2avy A1555 3Pout A1659, A1660, A1661, A1662, A1663, A1664 A:A1204, G:A1048, U:A1049 2qou A1555 3Pout A1662, A1954, A1955, A1956, A1957, N101 U:A1049, A:A1204, G:A1048 2i2p A1555 3Pout A1660, A1661, A1662, A1663, A1664, A1665 A:A1204, G:A1048, U:A1049 2qow A1587 3Pout A2100, A2101, A2102, A2103, N266, N1813 G:A1048, U:A1049, A:A1204

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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