MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON 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 2 of 9 | « Previous | Next » | 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 A3510 Oph·Pout A:A2705(OP2) A5160, A5161, A5162, A5163 C:A2704 G:A2706, A:A2705 3v2d A3425 Oph·Pout G:A1647(OP2) A4918, A4919, A4920, A4921 G:A1325 A:A1616, C:A1646 A:A1616 3v2d A3413 Oph·Pout G:A1997(OP2) A4879, A4880, E412, E413 U:A1995 C:A1996 3v2d A3389 Oph·Pout U:A588(OP1) A4789, A4790, A4791, A4792, A4793 C:A664 C:A587 3v2d A3384 Oph·Pout A:A1156(OP2) A4772, A4773, A4774, A4775 A:A1155 G:A1157 3v2d A3416 Oph·Pout A:A1970(OP2) A4890, A4891, A4892, A4893, A4894 A:A1900 G:A1899, U:A1834 G:A1835 3v2d A3374 Oph·Pout G:A2251(OP1) A4741, A4742, A4743, A4744, A4745 G:A2252 U:A2249 G:A2252, G:A2253 3v2d A3331 Oph·Pout G:A1560(OP1) A4627, A4628, A4629, A4630 G:A1561 G:A1561 3v2d A3328 Oph·Pout C:A2879(OP2) A4615, A4616, A4617, A4618 U:A2878 A:A2835 3v2d A3526 Oph·Pout A:A945(OP2) A5207, A5208, A5209, A5210, A5211 G:A831 G:A944 G:A832, G:A944, G:A831 3v2d A3317 Oph·Pout G:A2719(OP2) A4577, A4578, A4579, A4580 U:A2687 U:A2688 3v2d A3311 Oph·Pout G:A2255(OP2) A4559, A4560, A4561, A4562 C:A2254 G:A2256, G:A2255 3v2d A3285 Oph·Pout G:A785(OP2) A4480, A4481, A4482, A4483 G:A792 C:A2440 C:A2440, G:A792 3v2d A3139 Oph·Pout G:A205(OP2) A4069, A4070, A4071, A4072 C:A203 C:A253 3v2d A3189 Oph·Pout G:A131(OP1) A4212, A4213, A4214, A4215 G:A143 A:A1349 3v2d A3217 Oph·Pout C:A574(OP1) A4288, A4289, A4290, A4291, A4292 C:A2055 G:A2035, G:A2018 3v2d A3193 Oph·Pout A:A53(OP2) A4220, A4221, A4222, A4223 A:A52 G:A54, G:A55 3v2d A3144 Oph·Pout A:A1001(OP2) A4083, A4084, A4085, A4086 A:A1000 G:A1003, G:A1002 3v2d B211 Oph·Pout A:B25(OP1) B314, B315, B316, B317 U:B55 G:B24 3v2d A3108 Oph·Pout U:A193(OP1) A3979, A3980, A3981, A3982 G:A2070 U:A803 U:A803

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].

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