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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 2z4m




2Z4M (4.45Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with paromomycin and ribosome recycling factor (rrf). this file contains the 30s subunit of the second 70s ribosome, with paromomycin bound. the entire crystal structure contains
List of all 59 Mg2+ binding sites in the PDB structure 2z4m 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2z4m A1579 Ob G:A1370(O6) A1785, A1786, A1787, A1788, A1789 U:A1351, G:A1371
2z4m A1604 Ob G:A1417(O6) A1901, A1902, A1903, A1904, A1905 G:A1415 G:A1482, G:A1416
2z4m A1550 Nb G:A362(N7) A1634, A1635, A1636, A1637, L124 G:A361, G:A362 G:A361
2z4m A1584 Nb G:A324(N7) A1805, A1806, A1807, A1808, A1809 U:A323, G:A324, G:A326
2z4m A1577 2Nb G:A858(N7), G:A869(N7) A1775, A1776, A1777, A1778 G:A869, G:A858, C:A868, C:A857
2z4m A1586 Oph A:A608(OP2) A1814, A1815, A1816, A1817, A1818 A:A630, A:A609, C:A631, U:A610
2z4m A1565 Oph A:A937(OP2) A1704, A1705, A1706, A1707, A1708 G:A939, A:A937, A:A938
2z4m A1597 Oph·Pout C:A536(OP1) A1866, A1867, A1868, A1869, A1870 C:A504 C:A522
2z4m A1594 Oph·Pout G:A100(OP2) A1851, A1852, A1853, A1854, A1855 A:A101 G:A64, A:A101, G:A102
2z4m A1582 Oph·Pout A:A1433(OP2) A1796, A1797, A1798, A1799, A1800 A:A1434 A:A1434, G:A1435
2z4m A1575 Oph·Pout G:A21(OP1) A1766, A1767, A1768, A1769, A1770 U:A561 G:A568, G:A567 A:A573, G:A567
2z4m A1574 Oph·Pout A:A572(OP1) A1761, A1762, A1763, A1764, A1765 A:A573 A:A819
2z4m A1554 Oph·Pout C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 A:A1196
2z4m A1599 Oph·Pout C:A352(OP2) A1874, A1875, A1876, A1877, A1878 G:A354 C:A330, C:A352 C:A330, A:A59, G:A354
2z4m A1553 Oph·Pout C:A934(OP1) A1650, A1651, A1652, A1653, A1654 U:A1345
2z4m A1603 Oph·Pout C:A980(OP1) A1896, A1897, A1898, A1899, A1900 A:A1219 G:A1220, G:A1221, A:A1219
2z4m A1590 Oph·2Pout U:A1224(OP1) A1832, A1833, A1834, A1835 G:A951, U:A952 C:A1223
2z4m A1587 Oph·2Pout A:A1110(OP2) A1819, A1820, A1821, A1822, A1823 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
2z4m A1561 Oph·2Pout C:A578(OP1) A1684, A1685, A1686, A1687, A1688 C:A817, U:A820 G:A575, C:A576
2z4m A1544 Oph·2Pout U:A891(OP2) A1605, A1606, A1607, A1608, A1609 A:A892, G:A903 U:A905, U:A904

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>