`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 4gas



4GAS (3.3Å) -- RIBOSOME/ANTIBIOTIC : Allosteric control of the ribosome by small-molecule antibiotics
List of all 39 Mg2+ binding sites in the PDB structure 4gas in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 2 | « Previous | | 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
4gas A1639 Ob G:A1417(O6) A1879, A1880, A1881, A1882, A1883 G:A1415, G:A1416 G:A1482, G:A1416
4gas A1601 Ob U:A180(O4) A1714, A1715, A1716, T201 A:A195, C:A178, A:A179, C:A194 A:A179
4gas A1609 Nb G:A324(N7) A1739, A1740, A1741, A1742, A1743 U:A323
4gas A1625 Nb G:A858(N7) A1819, A1820, A1821, A1822 G:A858, G:A869, C:A868 G:A869
4gas A1611 Nb G:A362(N7) A1749, A1750, A1751, A1752, A1753
4gas A1603 Nb G:A64(N7) A1706, A1707, A1708, A1709, A1710 G:A100
4gas A1607 Oph G:A558(OP1) A1729, A1730, A1731, A1732 G:A297, G:A557 G:A299, A:A298
4gas A1602 Oph G:A21(OP1) A1701, A1702, A1703, A1704, A1705 G:A567, G:A568 A:A563, G:A567
4gas A1616 Oph·Pout A:A547(OP1) A1774, A1775, A1776, A1777, A1778 G:A548 G:A402, C:A403
4gas A1627 Oph·Pout C:A934(OP1) A1828, A1829, A1830, A1831, A1832 U:A1345
4gas A1628 Oph·Pout A:A937(OP2) A1833, A1834, A1835, A1836, A1837 A:A938 A:A938, G:A939
4gas A1635 Oph·Pout A:A1110(OP2) A1863, A1864, A1865, A1866, C301 A:A1111 A:A1111, U:A1189, A:A1188
4gas A1610 Oph·Pout C:A352(OP2) A1744, A1745, A1746, A1747, A1748 G:A354 G:A331, C:A330, C:A352 C:A330, G:A354
4gas A1626 Oph·2Pout U:A891(OP2) A1823, A1824, A1825, A1826, A1827 A:A892, G:A903 U:A904, U:A905, G:A903
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
4gas A1617 Oph·2Pout A:A560(OP2) A1779, A1780, A1781, A1782, L201 A:A563, G:A557 U:A565, A:A300
4gas A1613 Oph·2Pout A:A510(OP2) A1760, A1761, A1762, A1763 G:A506, A:A509 U:A508 A:A510
4gas A1619 Oph·3Pout C:A578(OP1) A1786, A1787, A1788, A1789, A1790 U:A820, C:A817, C:A576 G:A575
4gas A1641 Oph·Or G:A1505(OP1) A:A1507(O3') A1887, A1888, A1889 C:A1501, G:A1504 U:A1506

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>