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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v2d A3445 Ob U:A2593(O4) A4977, A4978, A4979, A4980, A4981 C:A2591, G:A2592 G:A2599, G:A2592, A:A1971
3v2d A3201 Ob G:A1814(O6) A4244, A4245, A4246, A4247, A4248 G:A1813 A:A1815, G:A1813
3v2d A3414 Ob G:A2685(O6) A4881, A4882, A4883, A4884, A4885 G:A2686, C:A2724
3v2d A3465 Ob U:A2419(O4) A5027, A5028, 8203, 8204, 8205 A:A2418
3v2d A3204 Ob G:A1822(O6) A4252, A4253, A4254, A4255 U:A1796, G:A1823, G:A1824
3v2d A3161 Ob U:A1263(O4) A4137, A4138, A4139, A4140 A:A2014, A:A2015 G:A1264, A:A1262
3v2d A3582 Ob G:A2371(O6) A5354, A5355, A5356, A5357 G:A2370, G:A2372, G:A2345
3v2d A3407 Nb G:A2032(N7) A4852, A4853, A4854, A4855, A4856 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
3v2d A3120 Nb G:A298(N7) A4011, A4012, A4013, A4014, A4015 C:A297, G:A298, G:A338
3v2d A3207 Nb G:A2002(N7) A4261, A4262, A4263, A4264, A4265 G:A2002, A:A2001 G:A2003
3v2d A3258 2Ob G:A1488(O6), U:A1489(O4) A4405, A4406, A4407, A4408 C:A1498 G:A1487, G:A1500
3v2d A3124 Ob·Nb G:A2303(O6) A4025, A4026, A4027, A4028 G:A2302
3v2d A3130 2Nb G:A733(N7), A:A761(N7) A4046, A4047, A4048, A4049 C:A732, G:A733, G:A760, A:A761
3v2d A3553 Oph A:A1890(OP2) A5270, A5271, A5272, A5273 G:A1850, U:A1851, G:A1891, C:A1852, A:A1889, A:A1890
3v2d A3438 Oph A:A2598(OP1) A4960, D409, D410, D411, D412
3v2d A3477 Oph A:A800(OP1) A5058, A5059, A5060, A5061 G:A799 C:A192, A:A800, A:A191
3v2d A3277 Oph C:A975(OP1) A4461, A4462, A4463, A4464, A4465 G:A974, A:A983
3v2d A3398 Oph G:A2035(OP1) A4822, A4823, A4824, A4825 G:A2037, G:A2024
3v2d A3300 Oph U:A1706(OP1) A4523, A4524, A4525, A4526 G:A1707, G:A1756
3v2d A3317 Oph·Pout G:A2719(OP2) A4577, A4578, A4579, A4580 U:A2687 U:A2688

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>