MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i20:A2945, See in JSmolClick on the image to toggle views Site type: Oph·Pout Schematic drawing for Oph·Pout List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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 6 of 53 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3i1z A1569 Oph·Pout U:A1095(OP2) A1741, A1742, A1743, A1744 C:A1096 G:A1094 C:A1109, G:A1108 2qoy A1569 Oph·Pout A:A768(OP2) A2031, A2032, A2033, A2034, A2035 U:A804 G:A769 2qp0 A1569 Oph·Pout A:A608(OP2) A2017, A2018, A2019, A2020, A2021 A:A607 G:A292 A:A630, A:A609, C:A631, U:A610 2i2p A1570 Oph·Pout A:A572(OP1) A1741, A1742, A1743, A1744, A1745 A:A573 A:A819 3ofo A1570 Oph·Pout G:A100(OP2) A1750, A1751, A1752, A1753, A1754 A:A101 G:A64, G:A100, A:A101, G:A102 2qoy A1570 Oph·Pout A:A572(OP1) A2036, A2037, A2038, A2039, A2040 G:A917 A:A819 2qbh A1570 Oph·Pout A:A572(OP1) A1736, A1737, A1738, A1739, A1740 A:A573 A:A819 3ofa A1571 Oph·Pout G:A100(OP2) A1754, A1755, A1756, A1757, A1758 A:A101 G:A64, G:A100, A:A101 3ofp A1571 Oph·Pout G:A100(OP2) A1747, A1748, A1749, A1750, A1751 A:A101 G:A64, A:A101 3ofx A1571 Oph·Pout G:A100(OP2) A1754, A1755, A1756, A1757, A1758 A:A101 G:A64, G:A100, A:A101 2qoy A1571 Oph·Pout G:A21(OP1) A2041, A2042, A2043, A2044, A2045 U:A561 G:A568, G:A567 A:A573, G:A567 2z4k A1571 Oph·Pout A:A572(OP1) A1741, A1742, A1743, A1744, A1745 A:A573 A:A819 3i1q A1572 Oph·Pout G:A100(OP2) A1750, A1751, A1752, A1753, A1754 A:A101 G:A64, G:A100, A:A101 3i21 A1572 Oph·Pout C:A352(OP2) A1771, A1772, A1773, A1774, A1775 G:A354 C:A330, C:A352 C:A330, G:A354, A:A59 3i1s A1572 Oph·Pout C:A352(OP2) A1769, A1770, A1771, A1772, A1773 G:A354 C:A352 G:A354, A:A59, C:A330 3i1o A1572 Oph·Pout C:A352(OP2) A1769, A1770, A1771, A1772, A1773 G:A354 C:A352 C:A330, G:A354, A:A59 3i1m A1572 Oph·Pout G:A100(OP2) A1755, A1756, A1757, A1758, A1759 A:A101 G:A64, G:A100, A:A101 3oaq A1572 Oph·Pout G:A100(OP2) A1755, A1756, A1757, A1758, A1759 A:A101 G:A64, G:A100, A:A101 3or9 A1572 Oph·Pout G:A100(OP2) A1754, A1755, A1756, A1757, A1758 A:A101 G:A64, G:A100, A:A101 3i1z A1572 Oph·Pout G:A100(OP2) A1753, A1754, A1755, A1756, A1757 A:A101 G:A64, G:A100, A:A101 2qbf A1573 Oph·Pout A:A572(OP1) A1763, A1764, A1765, A1766, A1767 A:A573 A:A819 2i2u A1573 Oph·Pout C:A352(OP2) A1740, A1741, A1742, A1743, A1744 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59 2qp0 A1573 Oph·Pout G:A100(OP2) A2037, A2038, A2039, A2040, A2041 A:A101 G:A64, G:A100, A:A101 2qow A1573 Oph·Pout G:A100(OP2) A2034, A2035, A2036, A2037, A2038 A:A101 G:A64, A:A101 2qbj A1573 Oph·Pout A:A572(OP1) A1761, A1762, A1763, A1764, A1765 A:A573 A:A819

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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