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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 3v2f



3V2F (2.7Å) -- RIBOSOME : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 2nd ribosome in the asu
List of all 136 Mg2+ binding sites in the PDB structure 3v2f in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 7 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v2f A3187 Ob G:A1382(O6) A3878, A3879, A3880, A3881 G:A1347, G:A1380 G:A1380, G:A1381
3v2f A3150 Ob U:A2593(O4) A3763, A3764, A3765, D408 G:A2592, C:A2591 A:A1971, G:A2599, G:A2592
3v2f A3570 Ob G:A2607(O6) A4997, A4998, A4999, A5000 G:A2608, G:A2588, U:A2605
3v2f A3374 Ob G:A928(O6) A4491, A4492, A4493, A4494, A4495 G:A848, U:A847, G:A927 G:A927
3v2f A3347 Ob G:A2371(O6) A4410, A4411, A4412, A4413, A4414 G:A2345, G:A2372
3v2f A3382 Ob G:A240(O6) A4513, A4514, A4515, A4516 A:A256 U:A239
3v2f A3201 Nb G:A2032(N7) A3920, A3921, A3922, A3923, A3924 G:A2032 A:A2453, C:A2055, C:A2499, A:A2572, G:A2454, U:A2500
3v2f A3205 Nb G:A2002(N7) A3939, A3940, A3941, A3942, A3943 G:A2002, A:A2001 G:A2003
3v2f A3232 Ob·Nb A:A1632(N7), G:A1633(O6) A4037, A4038, A4039, A4040 A:A1632, A:A1631 A:A1631, A:A1762
3v2f A3166 2Nb G:A733(N7), A:A761(N7) A3810, A3811, A3812, A3813 G:A760, A:A761, G:A733, C:A732
3v2f A3338 Oph A:A2227(OP2) A4383, A4384, A4385, A4386 C:A2226 G:A2090, U:A2092, A:A2227, G:A2228, U:A2091
3v2f A3271 Oph A:A53(OP2) A4174, A4175, A4176, A4177, A4178 G:A54, G:A55
3v2f A3489 Oph A:A311(OP2) A4812, A4813, A4814, A4815 U:A303, G:A304, U:A305
3v2f A3429 Oph A:A2598(OP1) A4640, D412, D413, D414
3v2f A3463 Oph A:A800(OP1) A4731, A4732, A4733, A4734, A4735 G:A799 C:A192, A:A191, A:A800
3v2f A3258 Oph C:A975(OP1) A4124, A4125, A4126, A4127 G:A974, A:A983
3v2f A3359 Oph·Pout A:A1664(OP2) A4446, A4447, A4448, A4449 G:A1992 G:A1667, A:A1664, G:A1992, G:A1666, A:A1665
3v2f A3357 Oph·Pout G:A2719(OP2) A4438, A4439, A4440, A4441, A4442 U:A2687 U:A2688
3v2f A3330 Oph·Pout G:A1975(OP2) A4358, A4359, A4360, A4361 C:A1771
3v2f A3313 Oph·Pout G:A785(OP2) A4298, A4299, A4300, A4301 G:A792 C:A2440 G:A792, C:A2440

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>