MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoy:A1566, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·Bout Schematic drawing for 2Pout·Rout·Bout List of all 32 Mg2+ binding sites with the site type 2Pout·Rout·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 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 2a43 A207 2Pout·Rout·Bout A208, A209, A210, A211, A212, A213 A:A23, C:A22 G:A6 A:A23 2qoy A1565 2Pout·Rout·Bout A2007, A2008, A2009, A2010, A2011, A2012 C:A726, G:A727 C:A853 G:A727 2qoy A1566 2Pout·Rout·Bout A2013, A2014, A2015, A2016, A2017, A2018 A:A1357, G:A1356 A:A1254 C:A1359 2z4m A1569 2Pout·Rout·Bout A1731, A1732, A1733, A1734, A1735, A1736 C:A726, G:A727 C:A853 G:A727 2qow A1591 2Pout·Rout·Bout A2120, A2121, A2122, A2123, A2124, A2125 G:A1356, A:A1357 A:A1254 C:A1359 4qcm A1734 2Pout·Rout·Bout A4046, A4047, A4048, A4049, A4050 A:A915, G:A916 U:A13 G:A916 3v2c A1735 2Pout·Rout·Bout A2157, A2158, A2159, A2160, A2161 A:A915, G:A916 U:A13 G:A916 4dv5 A1845 2Pout·Rout·Bout A2228, A2229, A2230, A2231, A2232 G:A1224, G:A951 C:A1223 A:A977 4dh9 A1885 2Pout·Rout·Bout A2119, A2120, A2121, A2122, A2123 A:A915, G:A916 U:A13 G:A916 3df1 A2143 2Pout·Rout·Bout A4144, A4145, A4146, A4147, A4148, A4149 A:A1357, G:A1356 A:A1254 C:A1359 2qan A2161 2Pout·Rout·Bout A2162, A2163, A2164, A2165, A2166, A2167 C:A726, G:A727 C:A853 G:A727 2qbb A2189 2Pout·Rout·Bout A2525, A2526, A2527, A2528, A2529, A2530 A:A768, C:A805 A:A767 G:A769 2qov B2908 2Pout·Rout·Bout B3032, B3033, B3034, B3035, B3036, B3037 C:B560, A:B1008 C:B1007 A:B1008 3i1p A2933 2Pout·Rout·Bout A3179, A3180, A3181, A3182 U:A810, U:A811 G:A1252 A:A1253 3ofz A2949 2Pout·Rout·Bout A3247, A3248, A3249, A3250, A3251 G:A1455, A:A1453 C:A1454 U:A1457 3ofr A2951 2Pout·Rout·Bout A3254, A3255, A3256, A3257, A3258 G:A1455, A:A1453 C:A1454 U:A1457 3i1r A2960 2Pout·Rout·Bout A3302, A3303, A3304, A3305, A3306, A3307 A:A1936, G:A1959 A:A1936 G:A1959 1vs6 B2968 2Pout·Rout·Bout B3315, B3316, B3317, B3318, B3319, B3320 C:B1376, C:B1351 U:B1352 G:B1377 3ofq A2989 2Pout·Rout·Bout A3439, A3440, A3441, A3442, A3443 A:A983, A:A572 G:A2029 U:A573 4too A3015 2Pout·Rout·Bout A3269, A3270, A3271, A3272, A3273, E303 U:A2016, G:A1256 U:A1255 U:A1255 4tpf A3016 2Pout·Rout·Bout A3269, A3270, A3271, A3272, A3273, E303 U:A2016, G:A1256 U:A1255 U:A1255 4tp7 A3016 2Pout·Rout·Bout A3269, A3270, A3271, A3272, E303, E304 U:A2016, G:A1256 U:A1255 U:A1255 4peb A3047 2Pout·Rout·Bout A3415, A3416, A3417, A3418, A3419 G:A1455, A:A1453 C:A1454 U:A1457 4qcq A3130 2Pout·Rout·Bout A4059, A4060, A4061, A4062, A4063 A:A915, G:A916 U:A13 G:A916 3v27 A3326 2Pout·Rout·Bout A3926, A3927, A3928, A3929, A3930, A3931 U:A464, G:A463 G:A1613 A:A789

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>