`

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 7 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 A3476 poly-nuclear Mg2+ site C:A1774(OP1) A5053, A5054, A5055, A5056, A5057 A:A1786, U:A1775 G:A1772 G:A1776, G:A1772
3v2d A3477 Oph A:A800(OP1) A5058, A5059, A5060, A5061 G:A799 C:A192, A:A800, A:A191
3v2d A3478 Oph·2Pout A:A2518(OP2) A5062, A5063, A5064, A5065 U:A2519, A:A2541 C:A2517 A:A2541
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 A3492 Oph·Ob C:A2248(OP2) U:A2249(O4) A5103, A5104, A5105, A5106 A:A2247, C:A2066, G:A2253
3v2d A3498 cis-2Oph A:A1269(OP2), A:A2005(OP1) A5120, A5121, A5122 A:A1268, C:A2006 A:A1269
3v2d A3499 2Pout·3Bout A5123, A5124, A5125, A5126, A5127 A:A2005, G:A2004 G:A1650, G:A1651, G:A1649
3v2d A3509 Oph·2Pout U:A1639(OP1) A5155, A5156, A5157, A5158, A5159 C:A1297, G:A1296 G:A2709 G:A2709
3v2d A3510 Oph·Pout A:A2705(OP2) A5160, A5161, A5162, A5163 C:A2704 G:A2706, A:A2705
3v2d A3512 3Pout·Rout·Bout A5167, A5168, A5169, A5170, A5171 C:A698, G:A1555, C:A697 A:A1554 A:A1554
3v2d A3514 cis-2Oph U:A1394(OP1), C:A1604(OP1) A5175, A5176, A5177, A5178 A:A1395
3v2d A3523 Oph·Pout A:A1664(OP2) A5196, A5197, A5198, A5199, A5200 G:A1992 G:A1992, A:A1665, G:A1666, G:A1667, A:A1664
3v2d A3526 Oph·Pout A:A945(OP2) A5207, A5208, A5209, A5210, A5211 G:A831 G:A944 G:A832, G:A944, G:A831
3v2d A3537 Oph·2Pout A:A802(OP1) A5233, A5234, A5235, A5236 G:A674, A:A675 A:A802, U:A803
3v2d A3540 poly-nuclear Mg2+ site A5242, A5243, A5244, A5245, A5432 A:A213, G:A177 G:A179, G:A180
3v2d A3548 fac-3Oph A:A2711(OP2), A:A2712(OP2), G:A2714(OP2) A5258, A5259, A5260 C:A2710, A:A2713
3v2d A3552 Mg2+ bound by non-RNA G:A585(OP2) A5268, A5269, U306, U307 THR:U6(OG1) C:A584, G:A1250, C:A1251 G:A585
3v2d A3553 Oph A:A1890(OP2) A5270, A5271, A5272, A5273 G:A1850, U:A1851, G:A1891, C:A1852, A:A1889, A:A1890
3v2d A3554 2Pout·3Bout A5274, A5275, A5276, A5277, A5278, A5279 A:A2360, C:A2359 U:A2357, A:A2361, C:A2356

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>