`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3q3z:A6, See in JSmolMgRNA representative site for type trans-2OP Click on the image to toggle views


Site type: trans-2Oph

Schematic drawing for
trans-2Oph
MgRNA type trans-2OP
List of all 282 Mg2+ binding sites with the site type trans-2Oph 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 12 | | | 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
3v2f A3242 trans-2Oph C:A1298(OP2), U:A1639(OP2) A4076, A4077, A4078, A4079 C:A1638, C:A1297 C:A2710 G:A1299
3v2f B208 trans-2Oph C:B30(OP1), A:B46(OP1) B323, B324, B325, B326 C:B31
3v2f A3300 trans-2Oph A:A751(OP1), A:A1614(OP1) A4262, A4263, A4264, A4265 G:A1613 A:A789, A:A1614, C:A1615, A:A751, C:A1617
462d B502 trans-2Oph G:A9(OP1), G:B9(OP1) A565, A597, B571, B594 G:A10, G:B10
4dha A3669 trans-2Oph U:A787(OP1), C:A790(OP2) A4627, A4628, A4629, A4630 C:A791, A:A789 A:A1780
4dhc A3503 trans-2Oph U:A2682(OP2), A:A2721(OP1) A4187, A4188, A4189, A4190 C:A2683, G:A2722
4dhc A3434 trans-2Oph C:A1298(OP2), U:A1639(OP2) A3974, A3975, A3976, A3977 C:A1297, C:A1638 C:A2710 G:A1299
4dr1 A1724 trans-2Oph A:A782(OP1), A:A794(OP1) A2103, A2104, A2105 C:A783 C:A1515 C:A1515
4dr2 A1623 trans-2Oph G:A117(OP2), G:A289(OP2) A2017, A2018, A2019, A2020 A:A116, A:A288 G:A117
4dr2 A1764 trans-2Oph A:A109(OP1), G:A331(OP2) A2433, A2434, A2435 G:A331
4dr2 A1772 trans-2Oph A:A782(OP1), A:A794(OP2) A2458, A2459, A2460, A2461 C:A783 G:A1521 G:A1521
4dr3 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1910, A1911, A1912, A1913 A:A116, A:A288 G:A117
4dr4 A1624 trans-2Oph G:A117(OP2), G:A289(OP2) A2014, A2015, A2016, A2017 A:A116, A:A288 G:A117, U:A118
4dr4 A1775 trans-2Oph A:A782(OP1), A:A794(OP2) A2362, A2363, A2364, A2365 C:A783 G:A1521, C:A1515 G:A1521
4dr5 A1665 trans-2Oph G:A506(OP1), A:A509(OP2) A2056, A2057, A2058 A:A510 A:A510
4dr5 A1713 trans-2Oph A:A782(OP1), A:A794(OP1) A2171, A2172, A2173, A2174 C:A783 G:A1521, C:A1515 G:A1521, C:A1515
4dr5 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1915, A1916, A1917, A1918 A:A116, A:A288 G:A117
4dr6 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A2015, A2016, A2017, A2018 A:A116, A:A288 G:A117
4duy A1658 trans-2Oph G:A506(OP1), A:A509(OP2) A2012, A2013, A2014 A:A510 A:A510
4duz A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118
4dv0 A1656 trans-2Oph G:A506(OP1), A:A509(OP2) A2007, A2008, A2009 A:A510 A:A510
4dv0 A1698 trans-2Oph A:A782(OP1), A:A794(OP1) A2079, A2080, A2081 C:A783 C:A1515 C:A1515
4dv2 A1660 trans-2Oph G:A506(OP1), A:A509(OP2) A2014, A2015, A2016 A:A510 A:A510
4dv2 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117, U:A118
4dv3 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117

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>