MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qp1:B2994, See in JSmolClick on the image to toggle views Site type: Oph·4Pout Schematic drawing for Oph·4Pout List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 10 | « 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 3la5 A11 Oph·4Pout G:A44(OP1) A9, A191, A302, A411, A412 C:A50, G:A44, C:A51, A:A45 3or9 A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 G:A566 3i1m A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 3oaq A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 3ofx A1540 Oph·4Pout A:A560(OP2) A1607, A1608, A1609, A1610, A1611 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 2qbj A1547 Oph·4Pout A:A560(OP2) A1623, A1624, A1625, A1626, A1627 U:A562, A:A563, G:A557, G:A558 A:A559 2z4m A1548 Oph·4Pout A:A560(OP2) A1623, A1624, A1625, A1626, A1627 U:A562, A:A563, G:A558, G:A557 A:A559 2qbh A1549 Oph·4Pout A:A560(OP2) A1635, A1636, A1637, A1638, A1639 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 2qou A1549 Oph·4Pout A:A560(OP2) A1928, A1929, A1930, A1931, A1932 U:A562, A:A563, G:A557, G:A558 A:A559 2qoy A1549 Oph·4Pout A:A560(OP2) A1930, A1931, A1932, A1933, A1934 U:A562, A:A563, G:A557, G:A558 A:A559 2z4k A1550 Oph·4Pout A:A560(OP2) A1635, A1636, A1637, A1638, A1639 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 3i1s A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, U:A1199, C:A1054 3i1o A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199 3i21 A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199 3oar A1561 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199 3ofb A1562 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199 3ofy A1562 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199 3ora A1562 Oph·4Pout G:A1198(OP1) A1717, A1718, A1719, A1720 A:A964, U:A965, C:A1054, U:A1199 3ofp A1562 Oph·4Pout G:A1198(OP1) A1709, A1710, A1711, A1712 A:A964, U:A965, C:A1054, U:A1199 2qp0 A1576 Oph·4Pout C:A536(OP1) A2047, A2048, A2049, A2050, A2051 C:A504, G:A537, A:A523, C:A503 C:A522 4tou A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566 4tp4 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566 4tp0 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566 4tol A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A558, G:A557 4tpc A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566

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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