MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2v:B2921, See in JSmolClick on the image to toggle views Site type: 2Nb Schematic drawing for 2Nb List of all 158 Mg2+ binding sites with the site type 2Nb 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 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3i21 A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869, C:A857 3i1s A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869, C:A857 3i1o A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869 3ofo A1557 2Nb G:A858(N7), G:A869(N7) A1695, A1696, A1697, A1698 G:A858, G:A869, C:A868 3ofa A1558 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, G:A869, C:A868 3ofx A1558 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, G:A869, C:A857, C:A868 3oar A1558 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, C:A868, G:A869 3oaq A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A857, C:A868 3ofp A1559 2Nb G:A858(N7), G:A869(N7) A1694, A1695, A1696, A1697 G:A858, G:A869, C:A868 3ofy A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, G:A869, C:A868 3or9 A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A868 3i1z A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, C:A857, C:A868 3ofb A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, C:A868, G:A869 3i1q A1559 2Nb G:A858(N7), G:A869(N7) A1695, A1696, A1697, A1698 G:A858, C:A857, C:A868 3i1m A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A868 2i2u A1560 2Nb G:A858(N7), G:A869(N7) A1682, A1683, A1684, A1685 G:A869, G:A858, C:A868, C:A857 2qp0 A1564 2Nb G:A858(N7), G:A869(N7) A1995, A1996, A1997, A1998 G:A869, G:A858, C:A868 2avy A1572 2Nb G:A858(N7), G:A869(N7) A1746, A1747, A1748, A1749 G:A858, G:A869, C:A868 2i2p A1573 2Nb G:A858(N7), G:A869(N7) A1755, A1756, A1757, A1758 G:A858, G:A869, C:A868 C:A857 2qbh A1573 2Nb G:A858(N7), G:A869(N7) A1750, A1751, A1752, A1753 G:A858, G:A869, C:A868 2qoy A1573 2Nb G:A858(N7), G:A869(N7) A2050, A2051, A2052, A2053 G:A858, G:A869, C:A868 1vs5 A1574 2Nb G:A858(N7), G:A869(N7) A1752, A1753, A1754, A1755 G:A858, G:A869, C:A868 2z4k A1574 2Nb G:A858(N7), G:A869(N7) A1755, A1756, A1757, A1758 G:A858, G:A869, C:A868 2qbf A1576 2Nb G:A858(N7), G:A869(N7) A1777, A1778, A1779, A1780 G:A869, G:A858, C:A868, C:A857 2qbj A1576 2Nb G:A858(N7), G:A869(N7) A1775, A1776, A1777, A1778 G:A869, G:A858, C:A868, C:A857

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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