MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2237, See in JSmolClick on the image to toggle views Site type: Oph·Ob Schematic drawing for Oph·Ob List of all 554 Mg2+ binding sites with the site type Oph·Ob in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 1 of 23 | « 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 2qbz X206 Oph·Ob A:X80(OP2) U:X81(O4) X325, X326, X327, X328 A:X61 3v2f B207 Oph·Ob A:B57(OP2) G:B23(O6) B319, B320, B321, B322 A:B58 G:B56 U:B22, A:B59 2yif Z1115 Oph·Ob A:Z92(OP1) U:Z89(O4) Z2006, Z2007, Z2011, Z2012 G:Z88 2yie Z1116 Oph·Ob A:Z92(OP1) U:Z89(O4) Z2011, Z2012, Z2013, Z2014 G:Z88 3i1o A1561 Oph·Ob G:A558(OP1) G:A299(O6) A1722, A1723, A1724, E198 A:A300 2i2u A1562 Oph·Ob G:A558(OP1) G:A299(O6) A1691, A1692, A1693, A1694 A:A560 G:A297 A:A300, G:A566 3oar A1563 Oph·Ob G:A558(OP1) G:A299(O6) A1720, A1721, A1722, E187 G:A297 G:A566 3i1o A1563 Oph·Ob A:A533(OP1) U:A516(O4) A1730, A1731, A1732, A1733 G:A515, G:A517 3i21 A1563 Oph·Ob A:A533(OP1) U:A516(O4) A1731, A1732, A1733, A1734 G:A517, G:A515 3i1s A1563 Oph·Ob A:A533(OP1) U:A516(O4) A1730, A1731, A1732, A1733 G:A515, G:A517 3ofp A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1718, A1719, A1720, E187 A:A560 G:A297 2i2u A1564 Oph·Ob A:A533(OP1) U:A516(O4) A1700, A1701, A1702, A1703 G:A517, G:A515 3ofy A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1720, A1721, A1722, E187 G:A297 A:A300, A:A298 3ofb A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1720, A1721, A1722, E187 A:A560 A:A300, G:A566 3i1z A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1718, A1719, A1720, A1721 A:A560 G:A297 A:A298, G:A566 3ofo A1564 Oph·Ob A:A533(OP1) U:A516(O4) A1725, A1726, A1727, A1728 A:A532 G:A517 3oar A1565 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A515, G:A517 3ofa A1565 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A515, G:A517 3ofx A1565 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A517 2qp0 A1566 Oph·Ob G:A558(OP1) G:A299(O6) A2004, A2005, A2006, A2007 A:A560 G:A297 A:A298, G:A566 3or9 A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1729, A1730, A1731, A1732 G:A515, G:A517 3i1z A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1727, A1728, A1729, A1730 C:A514, G:A515 G:A515 3ofy A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A515, G:A517 3i1q A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1725, A1726, A1727, A1728 A:A532 3ofp A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1725, A1726, A1727, A1728 G:A515, G:A517

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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