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 9 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 A3696 4Pout·2Bout A5676, A5677, A5678, A5679 G:A2578, A:A2051, U:A2613, A:A2614 A:A2051, A:A2614 3v2d A3650 5Pout A5501, A5502, A5503, A5504, A5505, A5506 G:A1606, G:A1303, A:A1608, C:A1304, C:A1607 3v2d A3390 Mg2+ bound by non-RNA G:A1192(N7) A4794, A4795, A4796, P313 HIS:P27(NE2) G:A1192, G:A1191 G:A1193, G:A1191 3v2d A3305 Mg2+ bound by non-RNA C:A2612(OP1) A4537, A4538, A4539, A4540 HIS:E132(NE2) U:A2611, G:A745 A:A746 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 E306 Mg2+ bound by non-RNA A4875, A4876, E410, E411 ASP:E127(OD2) G:A1992 G:A1997 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 A3618 poly-nuclear Mg2+ site G:A212(OP2) A5244, A5432, A5433, A5434, A5435 G:A177, A:A213, G:A178 3v2d A3600 poly-nuclear Mg2+ site A5320, A5388, A5389, A5390, A5391, A5392 G:A495, G:A496 3v2d A3570 poly-nuclear Mg2+ site A:A503(O2') A5320, A5321, A5322, A5323 G:A506 3v2d B212 poly-nuclear Mg2+ site B318, B319, B320, B321, B322 G:B81 G:B82, G:B83 3v2d A3152 poly-nuclear Mg2+ site G:A1776(OP2) A4107, A4108, A4109, A4110, A4111 A:A1981, U:A1775 G:A1776 3v2d A3443 poly-nuclear Mg2+ site A4970, A4971, A4972, A4973, A4974 G:A1358, U:A1357, C:A1370 G:A1371 3v2d A3403 poly-nuclear Mg2+ site C:A453(OP1) G:A450(O6) A4844, A4845, A4846 A:A449, A:A454 A:A449 3v2d A3472 poly-nuclear Mg2+ site G:A1714(O6) A5043, A5044, A5045, A5046 G:A1717 3v2d A3655 poly-nuclear Mg2+ site A5519, A5520, A5521, A5522, A5523 G:A186, G:A187 G:A186, G:A187, G:A188, G:A189 3v2d A3540 poly-nuclear Mg2+ site A5242, A5243, A5244, A5245, A5432 A:A213, G:A177 G:A179, G:A180

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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