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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 3v2d




3V2D (2.7Å) -- RIBOSOME : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu
List of all 177 Mg2+ binding sites in the PDB structure 3v2d 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 4 of 9 | | | 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
3v2d A3194 Oph·2Pout G:A446(OP2) A4224, A4225, A4226, A4227, A4228 C:A445, C:A1200 U:A1199 G:A446
3v2d A3156 Oph·2Pout C:A574(OP2) A4120, A4121, A4122, A4123, A4124 G:A573, U:A576 G:A577, U:A576, G:A563
3v2d A3248 Oph·2Pout G:A1209(OP2) A4376, A4377, A4378, A4379 C:A313, A:A1210 A:A331, G:A1209
3v2d A3267 Oph·2Pout A:A1237(OP1) A4434, A4435, A4436, A4437, A4438 G:A476, A:A477
3v2d A3171 Oph·2Pout G:A2349(OP1) A4169, A4170, A4171, A4172 A:A2418, C:A2350
3v2d A3166 Oph·2Pout C:A1013(OP2) A4153, A4154, A4155, A4156 U:A1014, A:A1143
3v2d A3126 Oph·3Pout C:A31(OP1) A4033, A4034, A4035, A4036, A4151 G:A1239, U:A1199, U:A1240 A:A1214
3v2d A3428 Oph·3Pout U:A2016(OP1) A4928, A4929, A4930, A4931 A:A2058, A:A2059, U:A2017
3v2d A3423 Oph·3Pout U:A2074(OP1) A4912, A4913, A4914, D408 U:A2075, C:A2240, G:A2239
3v2d A3143 Oph·3Pout C:A192(OP1) A4078, A4079, A4080, A4081, A4082 A:A199, U:A2243, U:A193 U:A193
3v2d A3376 Oph·3Pout U:A2406(OP1) A4750, A4751, A4752, A4753, A4754 G:A2407, U:A2408, G:A2409 G:A2405 G:A2410, U:A2408, G:A2409
3v2d A3367 Oph·3Pout G:A563(OP2) A4718, A4719, A4720, A4721 C:A564, A:A572, G:A975 C:A975
3v2d A3219 Oph·3Pout A:A2062(OP2) A4298, A4299, A4300, A4301, A4302 G:A2444, C:A2443, G:A2061 G:A2444, G:A2445
3v2d A3411 Oph·4Pout G:A741(OP1) A4865, A4866, A4867, A4868, A4869 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
3v2d A3329 Oph·4Pout G:A862(OP2) A4619, A4620, A4621, A4622, A4623 A:A861, A:A910, A:A863, A:A909 G:A862, A:A863
3v2d A3118 Oph·4Pout U:A963(OP1) A4004, A4005, A4006, A4007, A4008 C:A964, C:A2498, A:A2497, G:A947
3v2d A3218 Oph·4Pout U:A2017(OP1) A4293, A4294, A4295, A4296, A4297 A:A578, G:A577, A:A2058, G:A2018
3v2d A3408 Oph·Ob A:A2033(OP1) U:A2028(O4) A4857, A4858, A4859, A4860 G:A2027, G:A2029
3v2d A3356 Oph·Ob G:A818(OP2) G:A1187(O6) A4679, A4680, A4681, A4682 C:A817, G:A1186 G:A818, G:A1186
3v2d A3253 Oph·Ob A:A973(OP2) U:A568(O4) A4391, A4392, A4393, A4394 G:A570, A:A571

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>