MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2v:B2959, See in JSmolClick on the image to toggle views Site type: Pout·Rout·3Bout Schematic drawing for Pout·Rout·3Bout List of all 32 Mg2+ binding sites with the site type Pout·Rout·3Bout 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1fuf A97 Pout·Rout·3Bout A92, A93, A96, B94, B95 U:A7 U:A6 U:B17, G:B15, G:B16 1vs5 A1599 Pout·Rout·3Bout A1872, A1873, A1874, A1875, A1876, A1877 C:A1400 C:A1399 G:A926, G:A1505, C:A1399 2i2v B2959 Pout·Rout·3Bout B3286, B3287, B3288, B3289, B3290, B3291 A:B582 C:B1251 C:B584, A:B582, G:B583 2qow A1546 Pout·Rout·3Bout A1896, A1897, A1898, A1899, A1900, A1901 G:A803 G:A803 U:A772, G:A773, G:A771 2qp1 B2957 Pout·Rout·3Bout B3773, B3774, B3775, B3776, B3777, B3778 A:B2386 U:B2384 C:B2326, U:B2387, A:B2386 2z4l B2983 Pout·Rout·3Bout B3380, B3381, B3382, B3383, B3384, B3385 A:B2386 U:B2384 C:B2326, A:B2386, U:B2387 3df1 A2219 Pout·Rout·3Bout A4220, A4221, A4222, A4223, A4224, A4225 U:A916 U:A13 U:A13, U:A916, G:A917 3i1r A2941 Pout·Rout·3Bout A3214, A3215, A3216, A3217, A3218, A3219 U:A1267 G:A1266 G:A2010, U:A2011, G:A2012 3oat A2982 Pout·Rout·3Bout A3399, A3400, A3401, A3402, A3403, A3404 C:A2055 A:A2054 U:A2034, G:A2035, A:A574 3oat A2940 Pout·Rout·3Bout A3206, A3207, A3208, A3209, A3210, A3211 U:A1267 G:A1266 G:A2010, U:A2011, G:A2012 3ofr A2984 Pout·Rout·3Bout A3409, A3410, A3411, A3412, A3413, A3414 C:A2055 A:A2054 U:A2034, G:A2035, A:A574 3ofz A2982 Pout·Rout·3Bout A3401, A3402, A3403, A3404, A3405, A3406 C:A2055 A:A2054 U:A2034, G:A2035, A:A574 3v27 A3573 Pout·Rout·3Bout A4976, A4977, A4978, A4979 U:A1955 G:A1954 G:A1950, G:A1948, G:A1949 3v27 A3597 Pout·Rout·3Bout A5056, A5057, A5058, A5059 G:A582 C:A1251 G:A582, G:A583, G:A585 4bpe A5001 Pout·Rout·3Bout A2148, A2149, A2161, A2162, A2163, A2245 G:A854 U:A913 G:A854, U:A913, A:A911 4bpn A5001 Pout·Rout·3Bout A6006, A6007, A6008, A6009, A6010, A6011 G:A854 U:A913 U:A913, G:A854, A:A911 4bpn A5025 Pout·Rout·3Bout A6433, A6434, A6435, A6436, A6437, A6438 C:A419 C:A416 G:A421, C:A416, A:A420 4bpo A5025 Pout·Rout·3Bout A2067, A2068, A2069, A2070, A2071, A2072 C:A419 C:A416 G:A421, C:A416, A:A420 4bpp A5001 Pout·Rout·3Bout A7027, A7028, A7029, A7030, A7031, A7032 G:A854 U:A913 U:A913, G:A854, A:A911 4dha A3742 Pout·Rout·3Bout A4879, A4880, A4881, A4882 U:A1955 G:A1954 G:A1948, G:A1949, G:A1950 4gar A3092 Pout·Rout·3Bout A3632, A3633, A3634, A3635 A:A1439 U:A1438 U:A1440, A:A1552, A:A1551 4gau A3078 Pout·Rout·3Bout A3572, A3573, A3574, A3575, A3576, A3577 U:A2034 A:A2054 G:A2035, A:A574, U:A2034 4nvw A3102 Pout·Rout·3Bout A4063, A4064, A4065, A4066 G:A21 G:A567 A:A573, A:A563, G:A567 4nvx A3294 Pout·Rout·3Bout A4147, A4148, A4149, A4150 C:A1333 U:A1313 U:A1335, G:A1334, U:A1316 4nw0 A3102 Pout·Rout·3Bout A4063, A4064, A4065, A4066 G:A21 G:A567 G:A567, A:A573, A:A563

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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