`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3r8s:A2930, See in JSmolMgRNA representative site for type OP             Click on the image to toggle views


Site type: Oph

Schematic drawing for
Oph

MgRNA type OP
List of all 588 Mg2+ binding sites with the site type Oph 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 2 of 24 | | | 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
1y26 X102 Oph A:X24(OP1) X273, X274, X275, X276, X277 G:X72, A:X24
1y26 X105 Oph A:X23(OP2) X290, X291, X292, X293, X294 U:X22 A:X21
1yls B240 Oph U:B234(OP1) B345, B346, B347, B348, B349 G:B236, G:B237
1yls D340 Oph U:D234(OP1) D389, D390, D391, D392, D393 G:D236, G:D237
2avy A1554 Oph A:A937(OP2) A1654, A1655, A1656, A1657, A1658 G:A939
2avy A1590 Oph G:A100(OP2) A1829, A1830, A1831, A1832, A1833 G:A64, C:A99, G:A100, A:A101
2avy A1570 Oph G:A21(OP1) A1737, A1738, A1739, A1740, A1741 G:A567 A:A573, G:A567
2avy A1595 Oph C:A352(OP2) A1852, A1853, A1854, A1855, A1856 G:A331, C:A330 C:A330, G:A354, A:A59
2aw4 B2972 Oph A:B1678(OP2) B3332, B3333, B3334, B3335, B3336 A:B1679
2aw4 B2934 Oph U:B419(OP1) B3155, B3156, B3157, B3158, B3159 G:B230
2aw4 B2948 Oph U:B120(OP2) B3218, B3219, B3220, B3221, B3222 G:B122, G:B123, G:B121
2aw4 B3010 Oph A:B1676(OP2) B3490, B3491, B3492, B3493, B3494 C:B1675 A:B1677, A:B1676
2aw4 B2962 Oph A:B800(OP1) B3286, B3287, B3288, B3289, B3290 G:B799 A:B191, C:B192, A:B800
2aw7 A1564 Oph A:A937(OP2) A1708, A1709, A1710, A1711, A1712 G:A939
2aw7 A1575 Oph G:A21(OP1) A1770, A1771, A1772, A1773, A1774 G:A568, G:A567 A:A573, G:A567
2aw7 A1603 Oph C:A980(OP1) A1899, A1900, A1901, A1902, A1903 G:A1221, G:A1220, A:A1219
2aw7 A1574 Oph A:A572(OP1) A1765, A1766, A1767, A1768, A1769 U:A916 A:A819
2awb B2946 Oph U:B120(OP2) B3215, B3216, B3217, B3218, B3219 G:B122, G:B123
2awb B2965 Oph U:B419(OP1) B3309, B3310, B3311, B3312, B3313 G:B230
2awb B2922 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 G:B799 A:B191, C:B192, A:B800
2awb B2947 Oph A:B1678(OP2) B3220, B3221, B3222, B3223, B3224 A:B1679
2i2p A1591 Oph G:A100(OP2) A1838, A1839, A1840, A1841, A1842 G:A64, C:A99, G:A100, A:A101, G:A102
2i2p A1578 Oph A:A1433(OP2) A1776, A1777, A1778, A1779, A1780 A:A1434, G:A1435
2i2p A1571 Oph G:A21(OP1) A1746, A1747, A1748, A1749, A1750 G:A568, G:A567 A:A573, G:A567
2i2p A1596 Oph C:A352(OP2) A1861, A1862, A1863, A1864, A1865 G:A331, C:A330 A:A59, C:A330, G:A354

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>