MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 174 Mg2+ binding sites with the site type 4Pout 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 6 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 4ji6 A1629 4Pout A2064, A2065, A2066, A2067 C:A578, C:A817, G:A576, U:A820 4ji8 A1605 4Pout A2008, A2009, A2010, A2011 U:A652, C:A651, U:A751, G:A752 4ji8 A1642 4Pout A2080, A2081, A2082, A2083 G:A15, A:A16, U:A13, U:A14 4lf7 A1783 4Pout A1907, A1908, A1909, A1910, A1911, A1912 U:A13, U:A14, G:A15, A:A16 4lf8 A1783 4Pout A1907, A1908, A1909, A1910, A1911, A1912 U:A13, U:A14, G:A15, A:A16 4lf9 A1721 4Pout A1807, A1808, A1809, A1810, A1811, A1812 U:A13, U:A14, G:A15, A:A16 4nvu A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, G:A15, A:A16 4nvy A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, A:A16, G:A15 4nw1 A3611 4Pout A4830, A4831, A4832, A4833 G:A2000, A:A2001, A:A1654, A:A1655 4nxm A1652 4Pout A2000, A2001, A2002, A2003 G:A15, A:A16, U:A13, U:A14 4nxn A1695 4Pout A2077, A2078, A2153, A2154 G:A1048, U:A1049, C:A1203, A:A1204 4pe9 A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 U:A1049, C:A1203, A:A1204, G:A1048 4peb A3136 4Pout A3807, A3808, A3809, A3810, A3811, N204 G:A2819, C:A2874, G:A2838, A:A2820 4peb A3011 4Pout A3250, A3251, A3252, A3253, A3254, A3255 C:A560, A:A1008, G:A2038, G:A559 4pec A3024 4Pout A3310, A3312, A3313, C302, C303 G:A784, A:A2589, G:A2588, C:A2440 4pec A3057 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973 4pec A3055 4Pout A3447, A3448, A3449, A3450, A3451 A:A1772, A:A1773, G:A1828, G:A1972 4qcm A1768 4Pout A4125, A4126, A4127, A4128, A4129, A4130 U:A13, U:A14, G:A15, A:A16 4qcq A3168 4Pout A4148, A4149, A4150, A4151, A4152, A4153 U:A13, U:A14, G:A15, A:A16 4qcu A3161 4Pout A4118, A4119, A4120, A4121, A4122, A4123 U:A13, U:A14, G:A15, A:A16 4qcy A3181 4Pout A4121, A4122, A4123, A4124, A4125, A4126 U:A13, U:A14, G:A15, A:A16 4tol A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 U:A1049, C:A1203, A:A1204, G:A1048 4too A3058 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973 4too A3025 4Pout A3311, A3312, C303, C304 G:A784, G:A2588, C:A2440, G:A2599 4too A3057 4Pout A3452, A3453, A3454, A3455, A3456, A3457 G:A1959, A:A1937, C:A1958, A:A1936

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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