MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 4 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v29 A3452 2Pout A4225, A4226, A4227, A4228 G:A848, A:A849 3v29 A3588 2Pout A4722, A4723, A4724, A4725, A4726, A4727 U:A1976, A:A1977 3v27 A3639 2Pout A5282, A5283, A5284, Y301, Y302, Y303 U:A303, G:A304 3v27 8102 2Pout A4758, 6201, 8208, 8209, 8210, 8211 C:A2347, U:A2348 3v27 A3401 2Pout A4225, A4226, A4227, 8201, 8202 C:A624, G:A242 3v27 A3436 2Pout A4377, A4378, A4379, A4380, A4381 C:A2260, C:A825 3v27 A3520 2Pout A4729, A4730, A4731, A4732, A4733 G:A2004, U:A1273 3v27 A3537 2Pout A4812, A4813, A4814, A4815, A4816 C:A1761, U:A2712 3v27 A3586 2Pout A5019, A5020, A5021, R306 G:A2819, G:A2838 3v26 A1710 2Pout A1942, A1943, A1944, A1945, A1946 A:A397, G:A396 3v26 A1738 2Pout A2076, A2077, A2078, A2079, A2080, A2081 C:A784, G:A785 3v23 A3578 2Pout A4883, A4884, A4885, A4886, A4887, A4888 C:A2441, C:A2442 3v23 A3453 2Pout A4463, A4464, A4465, A4466, A4467 G:A1356, U:A773 3owz B114 2Pout B145, B146, B147, B148, B149, B150 A:B11, G:B10 3orb A2932 2Pout A3176, A3177, A3178, A3179, A3180, A3181 G:A822, A:A947 3og0 E202 2Pout A3106, A3107, A3108, A3109, A3110, A3111 U:A2016, G:A1256 3og0 A2906 2Pout A3048, A3049, A3050, A3051, A3052, A3053 C:A41, A:A42 3og0 A3027 2Pout A3599, A3600, A3601, A3602 U:A1188, A:A1189 3ofz A2931 2Pout A3171, A3172, A3173, A3174, A3175, A3176 G:A822, A:A947 3ofq A2962 2Pout A3310, A3311, A3312, A3313, A3314, A3315 A:A1916, U:A1915 3ofq A2937 2Pout A3199, A3200, A3201, A3202 G:A822, A:A945 3ofp A1 2Pout A2, A3, A4, A1576, A1577, T87 G:A259, G:A258 3ofd A3028 2Pout A3600, A3601, A3602, A3603 U:A1188, A:A1189 3ofd A2907 2Pout A3050, A3051, A3052, A3053, A3054, A3055 C:A41, A:A42 3ofc A2931 2Pout A3173, A3174, A3175, A3176, A3177, A3178 G:A822, A:A947

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>