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

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Representative site 2qp1:B2994, See in JSmolMgRNA representative site for type OP-4PO         Click on the image to toggle views


Site type: Oph·4Pout

Schematic drawing for
Oph·4Pout

MgRNA type OP-4PO
List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 7 of 10 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v27 A3488 Oph·4Pout G:A741(OP1) A4592, A4593, A4594, A4595, A4596 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
3v27 A3330 Oph·4Pout C:A409(OP1) A3943, A3944, A3945, A3946 C:A392, C:A375, C:A376, C:A393
3v29 A3347 Oph·4Pout C:A31(OP1) A3805, A3806, A3807, A3808, A3809 U:A1199, U:A1240, G:A1239, C:A1200 A:A1214
3v29 A3383 Oph·4Pout C:A1636(OP2) A3946, A3947, A3948, A3949, A3950 G:A1299, U:A1300, G:A1635, A:A1637 U:A1300
3v29 A3498 Oph·4Pout U:A2016(OP1) A4385, A4386, A4387, A4388, F405 A:A578, U:A2017, A:A2058, A:A2059 U:A1255 U:A1255
3v2d A3411 Oph·4Pout G:A741(OP1) A4865, A4866, A4867, A4868, A4869 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
3v2d A3218 Oph·4Pout U:A2017(OP1) A4293, A4294, A4295, A4296, A4297 A:A578, G:A577, A:A2058, G:A2018
3v2d A3329 Oph·4Pout G:A862(OP2) A4619, A4620, A4621, A4622, A4623 A:A861, A:A910, A:A863, A:A909 G:A862, A:A863
3v2d A3118 Oph·4Pout U:A963(OP1) A4004, A4005, A4006, A4007, A4008 C:A964, C:A2498, A:A2497, G:A947
3v2e A1694 Oph·4Pout U:A560(OP2) A2025, A2026, A2027, A2028 C:A562, A:A563, G:A557, G:A558 A:A559
3v2f A3179 Oph·4Pout G:A741(OP1) A3847, A3848, A3849, A3850, A3851 C:A1983, A:A1784, A:A1785, G:A2608 G:A2607
3v2f A3199 Oph·4Pout U:A2017(OP1) A3912, A3913, A3914, A3915 G:A577, A:A578, G:A2018, A:A2058
3v2f A3180 Oph·4Pout C:A31(OP1) A3852, A3853, A3854, A3855, A3856 U:A1199, C:A1200, U:A1240, G:A1239 A:A1214
4dha A3675 Oph·4Pout G:A741(OP1) A4654, A4655, A4656, A4657, A4658 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
4dha A3874 Oph·4Pout U:A1249(OP1) A5344, A5345, A5346, A5347, A5348 C:A587, G:A585, A:A586, G:A1250
4dhc A3392 Oph·4Pout G:A741(OP1) A3837, A3838, A3839, A3840, A3841 C:A1983, A:A1784, G:A2608, A:A1785
4dhc A3429 Oph·4Pout C:A1636(OP2) A3955, A3956, A3957, A3958 G:A1299, U:A1300, A:A1637, A:A1301
4dr1 A1633 Oph·4Pout U:A560(OP2) A1960, A1961, A1962, A1963 C:A562, G:A557, G:A558, A:A563
4duy A1627 Oph·4Pout U:A560(OP2) A1956, A1957, A1958, A1959 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4dv4 A1627 Oph·4Pout U:A560(OP2) A1952, A1953, A1954, A1955 C:A562, A:A563, G:A558, G:A557
4dv6 A1629 Oph·4Pout U:A560(OP2) A1953, A1954, A1955, A1956 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4gaq A1619 Oph·4Pout C:A578(OP1) A1785, A1786, A1787, A1788, A1789 U:A820, G:A821, C:A817, C:A576 G:A575
4gar A3047 Oph·4Pout U:A1647(OP2) A3421, A3422, A3423, A3424, A3425 U:A1325, A:A1272, A:A1618, C:A1617 C:A1646, A:A1616 A:A1616
4gar A3095 Oph·4Pout U:A1636(OP2) A3648, A3649, A3650, A3651, A3652 A:A1301, G:A1299, G:A1300, A:A1635
4gau A3053 Oph·4Pout G:A1828(OP1) A3452, A3453, A3454, A3455, A3456 A:A1772, A:A1773, G:A1972, G:A1973

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>