MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3v24 3V24 (3Å) -- RIBOSOME : Crystal structure of rmf bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound rmf of the 2nd ribosome in the asu List of all 11 Mg2+ binding sites in the PDB structure 3v24 in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v24 A1648 Nb G:A324(N7) A1741, A1742, T201, T202 G:A324 3v24 A1643 Oph C:A352(OP2) A1723, A1724, A1725, A1726 C:A352 C:A330, A:A59 3v24 A1663 Oph·2Pout G:A588(OP2) A1785, A1786, A1787, A1788 C:A645, G:A644 G:A587 3v24 A1666 Oph·3Pout A:A315(OP1) A1795, A1796, A1797, A1798 G:A316, G:A317, G:A318 G:A318, G:A319 3v24 A1644 2Bout A1727, A1728, A1729, A1730, A1731 G:A285, U:A287 3v24 A1670 2Bout A1812, A1813, A1814, A1815, A1816 G:A376, G:A377 3v24 A1645 Pout·2Bout A1732, A1733, A1734, A1735, A1736 G:A266 G:A258, G:A257 3v24 A1664 Pout·3Bout A1789, A1790, A1791, A1792 A:A753 C:A589, G:A650, G:A649 3v24 A1668 Pout·5Bout A1802, A1803, A1804, A1805, A1806, A1807 G:A1057 C:A1059, G:A1058, G:A1198, U:A1199, G:A1197 3v24 A1669 2Pout·2Bout A1808, A1809, A1810, A1811 G:A803, U:A804 G:A771, U:A772 3v24 A1662 3Pout·Bout A1781, A1782, A1783, A1784 A:A621, G:A617, C:A620 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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