MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbe:B3457, See in JSmolClick on the image to toggle views Site type: 2Pout·4Bout Schematic drawing for 2Pout·4Bout List of all 68 Mg2+ binding sites with the site type 2Pout·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 1 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3q3z V5 2Pout·4Bout V100, V104, V107, V108, V109, V110 C:V72, G:V73 G:V12, A:V74, A:V13, G:V73 4a17 063 2Pout·4Bout 05603, 05604, 05605, 05606, 05607, 05608 A:257, A:256 U:258, G:259, G:249, C:250 4a1a 063 2Pout·4Bout 05491, 05492, 05493, 05494, 05495, 05496 A:257, A:256 U:258, G:249, C:250, G:259 4gau B201 2Pout·4Bout B301, B302, B303, B304 A:B57, A:B58 U:B22, C:B60, G:B23, A:B59 4a1a 0325 2Pout·4Bout 07715, 07716, 07717, 07718, 07719, 07720 G:365, A:364 U:3109, G:3108, G:365, G:366 3or9 A1537 2Pout·4Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, C:A418, G:A416, U:A426 3ofx A1537 2Pout·4Bout A1592, A1593, A1594, A1595, A1596, A1597 A:A415, G:A416 G:A417, C:A418, G:A425, G:A416 2qbh A1548 2Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 2qou A1548 2Pout·4Bout A1922, A1923, A1924, A1925, A1926, A1927 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 3i21 A1553 2Pout·4Bout A1681, A1682, A1683, A1684, A1685, A1686 C:A797, A:A781 U:A798, G:A799, G:A800, C:A797 4tp8 A1604 2Pout·4Bout A1715, A1716, A1717, A1718, A1719, A1720 G:A416, A:A415 G:A416, G:A417, U:A426, G:A425 4gd1 A1604 2Pout·4Bout A1717, A1718, A1719, A1720, A1721, A1722 A:A415, G:A416 G:A416, G:A417, U:A426, G:A425 4tol A1604 2Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A416, G:A417, G:A425, U:A426 4tp0 A1604 2Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A417, C:A418, U:A426, G:A416 4tp2 A1612 2Pout·4Bout A1752, A1753, A1754, A1755, A1756, A1757 G:A416, A:A415 G:A417, G:A425, U:A426, G:A416 4pea A1612 2Pout·4Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A416, A:A415 G:A417, G:A425, U:A426, G:A416 4tpa A1622 2Pout·4Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, A:A807, G:A773 4tp2 A1622 2Pout·4Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, A:A807, G:A773 4ji1 A1756 2Pout·4Bout A2225, A2226, A2227, A2228, A2229, A2230 A:A431, G:A407 G:A409, G:A410, A:A408, G:A407 4dv0 A1810 2Pout·4Bout A2214, A2215, A2216, A2217, A2218 A:A759, G:A760 U:A580, G:A581, G:A579, G:A761 4dr1 A1814 2Pout·4Bout A2126, A2127, A2128, A2129 U:A264, G:A265 G:A190, G:A260, U:A261, G:A259 4dv6 A1838 2Pout·4Bout A2298, A2299, A2300, A2301, A2302, A2303 A:A759, G:A760 G:A579, U:A580, G:A761, C:A762 4ji0 A1858 2Pout·4Bout A2155, A2156, A2157, A2158, A2159, A2160 A:A609, G:A610 C:A612, G:A627, G:A628, U:A626 2qb9 A2031 2Pout·4Bout A2384, A2385, A2386, A2387, A2388, A2389 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 2qal A2031 2Pout·4Bout A2032, A2033, A2034, A2035, A2036, A2037 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646

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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