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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 5 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 A3408 Oph·Ob A:A2033(OP1) U:A2028(O4) A4857, A4858, A4859, A4860 G:A2027, G:A2029
3v2d A3365 cis-2Oph U:A576(OP1), A:A2503(OP1) A4712, A4713, A4714 G:A577, U:A2504
3v2d A3125 cis-2Oph C:A1670(OP1), U:A1671(OP2) A4029, A4030, A4031, A4032 G:A2550, G:A2549
3v2d A3359 cis-2Oph G:A2056(OP2), A:A2057(OP2) A4689, A4690, A4691, A4692 U:A2504, G:A2505 A:A2503 A:A2058, A:A2057
3v2d A3375 cis-2Oph G:A411(OP1), G:A2407(OP1) A4746, A4747, A4748, A4749 A:A412 U:A2406 G:A2407, U:A2408
3v2d A3378 cis-2Oph U:A2431(OP2), A:A2432(OP2) A4756, A4757, A4758, A4759 A:A2433 A:A2393
3v2d A3393 cis-2Oph A:A1009(OP2), A:A1010(OP2) A4805, A4806, A4807 C:A1006 A:A1010
3v2d A3399 cis-2Oph G:A2061(OP2), G:A2502(OP2) A4826, A4827, A4828, A4829 G:A2446 A:A2060, C:A2501 A:A2060, G:A2446, G:A2445
3v2d A3417 cis-2Oph A:A1970(OP1), A:A1971(OP1) A4895, A4896, A4897, A4898 A:A1969
3v2d A3460 cis-2Oph A:A2711(OP1), A:A2712(OP1) A5014, A5015, A5016, A5017 C:A1297
3v2d A3481 cis-2Oph A:A1268(OP1), C:A2006(OP1) A5073, A5074, A5075, A5076 G:A2049, G:A2048 U:A1267
3v2d A3483 cis-2Oph A:A1265(OP2), U:A2615(OP1) A5079, A5080, A5081, A5082 A:A2614 U:A1267
3v2d A3498 cis-2Oph A:A1269(OP2), A:A2005(OP1) A5120, A5121, A5122 A:A1268, C:A2006 A:A1269
3v2d A3514 cis-2Oph U:A1394(OP1), C:A1604(OP1) A5175, A5176, A5177, A5178 A:A1395
3v2d A3179 cis-2Oph G:A370(OP2), A:A422(OP2) A4188, A4189, A4190, A4191 A:A423 G:A370, C:A271, A:A423
3v2d A3240 cis-2Oph A:A2758(OP2), G:A2759(OP2) A4355, A4356, A4357, A4358 U:A2756 U:A2756, G:A2759
3v2d A3400 trans-2Oph U:A787(OP1), C:A790(OP2) A4830, A4831, A4832, A4833 C:A791, A:A789 A:A1780
3v2d A3154 trans-2Oph U:A1352(OP2), C:A1376(OP2) A4115, A4116, A4117, A4118 C:A1351, C:A1375 G:A1377
3v2d A3388 trans-2Oph A:A586(OP2), U:A1249(OP1) A4785, A4786, A4787, A4788 G:A1250, C:A587, G:A585
3v2d A3459 trans-2Oph C:A1298(OP2), U:A1639(OP2) A5010, A5011, A5012, A5013 C:A1638, C:A1297 C:A2710 G:A1299

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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