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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2925, See in JSmolMgRNA representative site for type OB Click on the image to toggle views


Site type: Ob

Schematic drawing for
Ob
MgRNA type OB
List of all 468 Mg2+ binding sites with the site type Ob 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 4 of 19 | | | 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
2qow A1581 Ob G:A1417(O6) A2072, A2073, A2074, A2075, A2076 G:A1416, G:A1415 G:A1482, G:A1416
2qp0 A1581 Ob G:A1417(O6) A2071, A2072, A2073, A2074, A2075 G:A1415, G:A1416 G:A1482, G:A1416
2qbh A1586 Ob G:A1108(O6) A1808, A1809, A1810, A1811 U:A1095 G:A1106, C:A1107
2qow A1594 Ob G:A1370(O6) A2138, A2139, A2140, A2141, A2142 U:A1372, U:A1351, G:A1371
2i2u A1594 Ob G:A1108(O6) A1847, A1848, A1849, A1850 U:A1095, C:A1096 G:A1094
2avy A1600 Ob U:A1358(O4) A1880, A1881, A1882, A1883, A1884 A:A1357 A:A1357, G:A976, C:A1359
2avy A1601 Ob G:A1417(O6) A1885, A1886, A1887, A1888, A1889 G:A1416, G:A1415 G:A1416, G:A1482
1vs5 A1601 Ob U:A1358(O4) A1884, A1885, A1886, A1887, A1888 A:A1357 C:A1359, A:A1357, G:A976
2qou A1601 Ob U:A1358(O4) A2180, A2181, A2182, A2183, A2184 A:A1357 C:A1359, A:A1357, G:A976
2qbh A1601 Ob U:A1358(O4) A1883, A1884, A1885, A1886, A1887 C:A1359, A:A1357
4gas A1601 Ob U:A180(O4) A1714, A1715, A1716, T201 A:A195, C:A178, A:A179, C:A194 A:A179
2i2p A1601 Ob G:A1417(O6) A1890, A1891, A1892, A1893, A1894 G:A1416, G:A1482
1vs5 A1602 Ob G:A1417(O6) A1889, A1890, A1891, A1892, A1893 G:A1416, G:A1415 G:A1482, G:A1416
4nxn A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
2qoy A1602 Ob G:A1417(O6) A2187, A2188, A2189, A2190, A2191 G:A1416, G:A1415 G:A1482, G:A1416
4duz A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 C:A372, G:A376
4dv5 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
2qou A1602 Ob G:A1417(O6) A2185, A2186, A2187, A2188, A2189 G:A1416, G:A1415 G:A1416, G:A1482
4dv1 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
2qbh A1602 Ob G:A1417(O6) A1888, A1889, A1890, A1891, A1892 G:A1416, G:A1415 G:A1416, U:A1481, G:A1482
4dv3 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
4dr3 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 C:A372, G:A376
2z4k A1603 Ob G:A1417(O6) A1892, A1893, A1894, A1895, A1896 G:A1416, G:A1415 G:A1482, G:A1416
2qbj A1603 Ob G:A1417(O6) A1897, A1898, A1899, A1900, A1901 G:A1415 G:A1482, G:A1416
2qbf A1603 Ob G:A1417(O6) A1902, A1903, A1904, A1905, A1906 G:A1415 G:A1482, G:A1415, G:A1416

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>