MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1603, See in JSmolClick on the image to toggle views Site type: cis-2Oph·2Ob Schematic drawing for cis-2Oph·2Ob List of all 28 Mg2+ binding sites with the site type cis-2Oph·2Ob 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs5 A1603 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1894, A1895 G:A1221, U:A982 1vs7 A1582 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1796, A1797 U:A982 G:A1221, U:A982 2avy A1576 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1765, A1766 G:A1221, U:A982 2j02 Z181 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 2qal A2210 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A2211, A2212 U:A982 G:A1221, U:A982 2qan A2236 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A2237, A2238 G:A1221, U:A982 2qbb A2236 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A2564, A2565 U:A982 G:A1221, U:A982 2qbd A2210 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A2211, A2212 U:A982 G:A1221, U:A982 2qbf A1580 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1796, A1797 G:A1221, U:A982 2qbj A1580 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1794, A1795 G:A1221, U:A982 2uua Z75 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 2uuc Z1134 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 2z4k A1578 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1774, A1775 U:A982 G:A1221, U:A982 2z4m A1581 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1794, A1795 G:A1221, U:A982 3df1 A2210 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A4211, A4212 U:A982 G:A1221, U:A982 3df3 A2236 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A4237, A4238 U:A982 G:A1221, U:A982 3i9d A1843 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 3ofx A1561 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1712, A1713 U:A982 G:A1221, C:A984 4b3r A2584 cis-2Oph·2Ob C:A979(OP1), C:A980(OP1) U:A981(O4), G:A1222(O6) 4cr1 A2685 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 4kj2 A1626 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 4kj6 A1626 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A1832 U:A982 U:A982 4lf9 A1693 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 4lfa A1677 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 4lfb A1710 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6)

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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