`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qam:B3090, See in JSmolMgRNA representative site for type OP-2PO Click on the image to toggle views


Site type: Oph·2Pout

Schematic drawing for
Oph·2Pout
MgRNA type OP-2PO
List of all 1607 Mg2+ binding sites with the site type Oph·2Pout 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 8 of 65 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tpe A1617 Oph·2Pout A:A560(OP2) A1778, A1779, A1780, A1781, A1782 U:A562, G:A558 A:A559 G:A566
4duz A1618 Oph·2Pout A:A768(OP2) A1937, A1938, A1939, A1940 C:A805, U:A804 A:A768, G:A769
4dr5 A1619 Oph·2Pout A:A768(OP2) A1948, A1949, A1950, A1951 A:A767, U:A804 A:A768, G:A769
4nxn A1620 Oph·2Pout A:A768(OP2) A1942, A1943, A1944, A1945 C:A805, U:A804 A:A768, G:A769
4gd2 A1621 Oph·2Pout A:A608(OP2) A1798, A1799, A1800, A1801, A1802 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
4ton A1621 Oph·2Pout A:A608(OP2) A1795, A1796, A1797, A1798, A1799 A:A607, A:A609 A:A609, U:A610, A:A630, A:A608
4tpe A1621 Oph·2Pout A:A608(OP2) A1797, A1798, A1799, A1800, A1801 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
4tpa A1621 Oph·2Pout A:A608(OP2) A1796, A1797, A1798, A1799, A1800 A:A607, A:A609 U:A610, A:A630, C:A631, A:A609
4pea A1621 Oph·2Pout A:A608(OP2) A1794, A1795, A1796, A1797, A1798 A:A607, A:A609 C:A631, A:A609, U:A610, A:A630, A:A608
4dr2 A1621 Oph·2Pout G:A750(OP2) A2011, A2012, A2013, A2014 C:A749, A:A653 G:A752
4tow A1621 Oph·2Pout A:A608(OP2) A1794, A1795, A1796, A1797, A1798 A:A607, A:A609 C:A631, A:A609, U:A610, A:A630, A:A608
4tp6 A1621 Oph·2Pout A:A608(OP2) A1796, A1797, A1798, A1799, A1800 A:A607, A:A609 A:A609, U:A610, A:A630, A:A608
4gas A1621 Oph·2Pout A:A608(OP2) A1797, A1798, A1799, A1800, A1801 A:A609, A:A607 A:A630, C:A631, A:A608, A:A609, U:A610
4gas A1624 Oph·2Pout A:A814(OP2) A1814, A1815, A1816, A1817, A1818 U:A904, G:A577
4ton A1624 Oph·2Pout A:A814(OP2) A1812, A1813, A1814, A1815, A1816 A:A815, G:A577 A:A816
4tp6 A1624 Oph·2Pout A:A814(OP2) A1813, A1814, A1815, A1816, A1817 A:A815, G:A577 A:A816
4gaq A1624 Oph·2Pout A:A814(OP2) A1812, A1813, A1814, A1815, A1816 G:A577, A:A815 A:A816
4pea A1624 Oph·2Pout A:A814(OP2) A1811, A1812, A1813, A1814, A1815 A:A815, G:A577 A:A816
4tpe A1624 Oph·2Pout A:A814(OP2) A1814, A1815, A1816, A1817, A1818 A:A815, G:A577 A:A816
4tpe A1626 Oph·2Pout U:A891(OP2) A1823, A1824, A1825, A1826, A1827 A:A892, G:A903 A:A906, U:A905, U:A904
4tow A1626 Oph·2Pout U:A891(OP2) A1820, A1821, A1822, A1823, A1824 A:A892, G:A903 A:A906, U:A905, U:A904
4pea A1626 Oph·2Pout U:A891(OP2) A1820, A1821, A1822, A1823, A1824 A:A892, G:A903 A:A906, U:A905, U:A904
4gas A1626 Oph·2Pout U:A891(OP2) A1823, A1824, A1825, A1826, A1827 A:A892, G:A903 U:A904, U:A905, G:A903
4ton A1626 Oph·2Pout U:A891(OP2) A1821, A1822, A1823, A1824, A1825 A:A892, G:A903 A:A906, U:A904, U:A905
4tpa A1626 Oph·2Pout U:A891(OP2) A1822, A1823, A1824, A1825, A1826 A:A892, G:A903 A:A906, U:A904, U:A905

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>