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 5 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 3og0 A2906 2Pout A3048, A3049, A3050, A3051, A3052, A3053 C:A41, A:A42 3orb A2932 2Pout A3176, A3177, A3178, A3179, A3180, A3181 G:A822, A:A947 3owz B114 2Pout B145, B146, B147, B148, B149, B150 A:B11, G:B10 3v23 A3453 2Pout A4463, A4464, A4465, A4466, A4467 G:A1356, U:A773 3v23 A3578 2Pout A4883, A4884, A4885, A4886, A4887, A4888 C:A2441, C:A2442 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 3v27 A3537 2Pout A4812, A4813, A4814, A4815, A4816 C:A1761, U:A2712 3v27 A3639 2Pout A5282, A5283, A5284, Y301, Y302, Y303 U:A303, G:A304 3v27 A3586 2Pout A5019, A5020, A5021, R306 G:A2819, G:A2838 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 8102 2Pout A4758, 6201, 8208, 8209, 8210, 8211 C:A2347, U:A2348 3v29 A3527 2Pout A4497, A4498, A4499, A4500, A4501, A4502 A:A289, A:A346 3v29 A3452 2Pout A4225, A4226, A4227, A4228 G:A848, A:A849 3v29 A3588 2Pout A4722, A4723, A4724, A4725, A4726, A4727 U:A1976, A:A1977 3v2d A3470 2Pout A5038, A5039, A5040, A5041, A5042 G:A2004, U:A1273 3v2d A3325 2Pout A4606, A4607, A4608, 1204 U:A2233, U:A380 3v2d 6102 2Pout A5066, A5067, A5068, 8206, 8207 C:A2347, U:A2419 3v2f A3519 2Pout A4891, A4892, A4893, A4894 G:A2839, G:A2872 4a1a 05 2Pout 05027, 05028, 05029, 05030, 05031, 05032 G:2137, U:2136 4a1c 070 2Pout 05347, 05348, 05349, 05350, 05351, 05352 A:25, A:24 4bpe A5060 2Pout A2361, A2362, A2363, A2367, A2439, A2440 A:A609, G:A610 4bpn A5060 2Pout A6229, A6230, A6231, A6232, A6233, A6234 A:A609, G:A610

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>