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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 3v23



3V23 (3Å) -- RIBOSOME : Crystal structure of rmf bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu
List of all 186 Mg2+ binding sites in the PDB structure 3v23 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 10 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v23 A3404 Or A:A528(O2') A4285, A4286, A4287, A4288, A4289 A:A529
3v23 A3407 Or U:A2406(O5') A4296, A4297, A4298, A4299, A4300 G:A2407, U:A2408, U:A2406 G:A2410, U:A2408, G:A2409
3v23 A3439 Ob G:A2685(O6) A4412, A4413, A4414, A4415 G:A2686, U:A2687, U:A2684
3v23 A3454 Ob U:A2593(O4) A4468, A4469, A4470, A4471 G:A2592 G:A2599, G:A2592, A:A1971
3v23 A3461 Ob U:A2419(O4) A4497, A4498, 8407, 8408
3v23 A3483 Ob G:A2371(O6) A4579, A4580, A4581, A4582 G:A2370
3v23 A3476 Ob G:A1651(O6) A4555, A4556, A4557, A4558, R305 G:A2004
3v23 A3492 Ob U:A1323(O4) A4618, A4619, A4620, A4621, A4622 A:A1322 C:A1320 C:A1320, A:A1322, G:A1328, G:A1324, C:A1330
3v23 A3321 Ob G:A1814(O6) A3961, A3962, A3963, A3964, A3965 G:A1813 A:A1815, G:A1813
3v23 A3324 Nb G:A2002(N7) A3975, A3976, A3977, A3978, A3979 G:A2002 G:A2003
3v23 A3539 Nb G:A2857(N7) A4755, A4756, A4757, A4758, A4759 G:A2859
3v23 A3432 Nb G:A2032(N7) A4383, A4384, A4385, A4386, A4387 G:A2032 G:A2454 C:A2055, C:A2499, A:A2453, U:A2500, A:A2572, G:A2454
3v23 A3354 Nb G:A974(N7) A4090, A4091, A4092, A4093, A4094 C:A971 G:A1186, G:A972
3v23 A3357 2Ob G:A538(O6), U:A555(O4) A4105, A4106, A4107, A4108 G:A539, U:A554
3v23 A3310 2Ob U:A594(O4), G:A662(O6) A3925, A3926, A3927, A3928 G:A593, G:A663, C:A664
3v23 A3302 2Nb G:A733(N7), A:A761(N7) A3894, A3895, A3896, A3897 C:A732, G:A733, G:A760, A:A761
3v23 A3413 Oph A:A1156(OP2) A4317, A4318, A4319, A4320, A4321 G:A997, C:A1158, G:A1157
3v23 A3368 Oph U:A1706(OP1) A4143, A4144, A4145, A4146 G:A1707, G:A1750
3v23 A3351 Oph C:A975(OP1) A4079, A4080, A4081, A4082 A:A983
3v23 A3317 Oph A:A53(OP2) A3947, A3948, A3949, A3950, A3951 G:A54

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>