MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoy:A1567, See in JSmolClick on the image to toggle views Site type: 2Bout Schematic drawing for 2Bout List of all 555 Mg2+ binding sites with the site type 2Bout 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 23 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v23 A3485 2Bout A4587, A4588, A4589, A4590, A4591 G:A2487, G:A2486 2qam B3464 2Bout B3991, B3992, B3993, B3994, B3995, B3996 G:B2549, G:B2550 2qba B3464 2Bout B3988, B3989, B3990, B3991, B3992, B3993 G:B2550, G:B2557 3v23 A3463 2Bout A4504, A4505, A4506, A4507, A4508 G:A36, G:A35 3v23 A3462 2Bout A4499, A4500, A4501, A4502, A4503 G:A1714, G:A1717 3v23 A3448 2Bout A4448, A4449, A4450, A4451, A4452 G:A743, G:A744 3v25 A3424 2Bout A4173, A4174, A4175, A4176, A4177, A4178 G:A1594, G:A1595 3v27 A3420 2Bout A4301, A4302, A4303, A4304, A4305 G:A2719, G:A2718 4nvv A3417 2Bout A4363, A4364, A4365, N3101, N3102 G:A2654, G:A2655 3v25 A3414 2Bout A4122, A4123, F404, F405 G:A798, G:A799 3v2f A3410 2Bout A4585, A4586, A4587, A4588 G:A1484, G:A1485 3v2d A3392 2Bout A4800, A4801, A4802, A4803, A4804 G:A2642, G:A2643 2qao B3389 2Bout B3939, B3940, B3941, B3942, B3943, B3944 G:B651, U:B652 3v27 A3388 2Bout A4174, A4175, A4176, A4177, A4178 G:A1163, G:A1162 3v29 A3387 2Bout A3967, A3968, A3969, A3970, A3971 G:A768, G:A769 3v23 A3384 2Bout A4209, A4210, A4211, A4212, A4213, A4214 G:A2830, G:A2831 3df4 B3382 2Bout B4383, B4384, B4385, B4386, B4387, B4388 G:B1259, U:B580 2qao B3382 2Bout B3933, B3934, B3935, B3936, B3937, B3938 G:B1259, U:B580 3v27 A3370 2Bout A4107, A4108, A4109, A4110, A4111 G:A521, G:A520 2qbc B3351 2Bout B3905, B3906, B3907, B3908, B3909 G:B2304, G:B2303 3v23 A3349 2Bout A4069, A4070, A4071, A4072, A4073 G:A1163, G:A1162 3df2 B3331 2Bout B4333, B4336, E4332, E4334, E4335, E4337 G:B797, G:B798 2qbe B3331 2Bout B3881, B3882, B3883, E203, E204, E205 G:B797, G:B798 2qam B3331 2Bout B3881, B3882, B3883, B3884, B3885, B3886 G:B797, G:B798 2qba B3331 2Bout B3881, B3882, B3883, E333, E334, E337 G:B798, G:B797

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>