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 1 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 6102 2Pout A5066, A5067, A5068, 8206, 8207 C:A2347, U:A2419 3v2d B211 Oph·Pout A:B25(OP1) B314, B315, B316, B317 U:B55 G:B24 3v2d B212 poly-nuclear Mg2+ site B318, B319, B320, B321, B322 G:B81 G:B82, G:B83 3v2d E306 Mg2+ bound by non-RNA A4875, A4876, E410, E411 ASP:E127(OD2) G:A1992 G:A1997 3v2d A3108 Oph·Pout U:A193(OP1) A3979, A3980, A3981, A3982 G:A2070 U:A803 U:A803 3v2d A3118 Oph·4Pout U:A963(OP1) A4004, A4005, A4006, A4007, A4008 C:A964, C:A2498, A:A2497, G:A947 3v2d A3120 Nb G:A298(N7) A4011, A4012, A4013, A4014, A4015 C:A297, G:A298, G:A338 3v2d A3121 Oph·2Pout U:A120(OP2) A4016, A4017, A4018, A4019, A4020 G:A121, G:A117 G:A122, G:A124, G:A123 3v2d A3124 Ob·Nb G:A2303(O6) A4025, A4026, A4027, A4028 G:A2302 3v2d A3125 cis-2Oph C:A1670(OP1), U:A1671(OP2) A4029, A4030, A4031, A4032 G:A2550, G:A2549 3v2d A3126 Oph·3Pout C:A31(OP1) A4033, A4034, A4035, A4036, A4151 G:A1239, U:A1199, U:A1240 A:A1214 3v2d A3130 2Nb G:A733(N7), A:A761(N7) A4046, A4047, A4048, A4049 C:A732, G:A733, G:A760, A:A761 3v2d A3137 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A4064, A4065 G:A194, A:A195 3v2d A3139 Oph·Pout G:A205(OP2) A4069, A4070, A4071, A4072 C:A203 C:A253 3v2d A3143 Oph·3Pout C:A192(OP1) A4078, A4079, A4080, A4081, A4082 A:A199, U:A2243, U:A193 U:A193 3v2d A3144 Oph·Pout A:A1001(OP2) A4083, A4084, A4085, A4086 A:A1000 G:A1003, G:A1002 3v2d A3149 3Pout·2Rout A4099, A4100, A4101, A4102, A4103 G:A690, A:A781, A:A782 U:A1777, G:A780 3v2d A3152 poly-nuclear Mg2+ site G:A1776(OP2) A4107, A4108, A4109, A4110, A4111 A:A1981, U:A1775 G:A1776 3v2d A3154 trans-2Oph U:A1352(OP2), C:A1376(OP2) A4115, A4116, A4117, A4118 C:A1351, C:A1375 G:A1377 3v2d A3156 Oph·2Pout C:A574(OP2) A4120, A4121, A4122, A4123, A4124 G:A573, U:A576 G:A577, U:A576, G:A563

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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