MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 5 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 4dr2 A1642 2Pout·Bout A2068, A2069, A2070, D404 A:A431, G:A407 A:A408 4dr2 A1657 2Pout·Bout A2108, A2109, A2110, A2111 U:A560, C:A562 G:A566 4dr2 A1630 2Pout·Bout A2039, A2040, A2041, A2042, A2043 C:A620, G:A617 G:A617 4dr2 A1736 2Pout·Bout A2333, A2334, A2335, A2336 U:A17, U:A13 U:A14 4dr4 A1941 2Pout·Bout A2398, A2399, A2400, A2401, A2402, A2403 U:A641, G:A594 G:A595 4dr4 A1730 2Pout·Bout A2247, A2248, A2249, A2250 G:A475, G:A476 G:A477 4dr4 A1631 2Pout·Bout A2032, A2033, A2034, D401, D402 C:A620, A:A621 G:A617 4dr5 A1799 2Pout·Bout A2186, A2187, A2188, A2189, A2190, A2191 G:A594, U:A641 G:A595 4dr5 A1841 2Pout·Bout A2432, A2433, A2434, A2435, A2436, A2437 U:A495, U:A437 G:A438 4dr5 A1612 2Pout·Bout A1933, A1934, A1935, A1936, A1937 C:A620, A:A621 G:A617 4dr7 A1820 2Pout·Bout A2486, A2487, A2488, A2489, A2490, A2491 G:A438, G:A492 G:A494 4duy A1799 2Pout·Bout A2164, A2165, A2166, A2167, A2168 G:A1385, G:A1386 G:A1386 4duy A1606 2Pout·Bout A1913, A1914, A1915, A1916 C:A651, G:A752 G:A752 4duz A1607 2Pout·Bout A1912, A1913, A1914, A1915 U:A652, C:A651 G:A752 4dv0 A1606 2Pout·Bout A1913, A1914, A1915, A1916 U:A652, C:A651 G:A752 4dv1 A1823 2Pout·Bout A2249, A2250, A2251, A2252, A2253 G:A1224, G:A951 A:A977 4dv2 A1818 2Pout·Bout A2205, A2206, A2207, A2208 A:A353, A:A53 A:A353 4dv5 A1607 2Pout·Bout A1912, A1913, A1914, A1915 C:A651, U:A751 G:A752 4gaq A1623 2Pout·Bout A1807, A1808, A1809, A1810, A1811, K201 U:A798, A:A780 G:A799 4gaq N201 2Pout·Bout A1844, A1845, A1846, N303, N304, N305 U:A1049, G:A1048 G:A1048 4gar A3114 2Pout·Bout A3719, A3720, A3721, A3722, A3723, A3724 U:A686, C:A687 G:A770 4gar A3090 2Pout·Bout A3620, A3621, A3622, A3623, A3624, A3625 U:A1409, G:A1408 G:A1410 4gar A3133 2Pout·Bout A3803, A3804, A3805, A3806, N201, N202 G:A2004, A:A1650 A:A1650 4gas A1632 2Pout·Bout A1849, A1850, A1851, A1852 C:A1054, A:A1197 U:A1199 4gau L201 2Pout·Bout A3289, A3290, A3291, L304 G:A622, C:A623 C:A624

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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