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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 9 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
4qct A3595 Oph·4Pout C:A1636(OP2) A4861, A4862, A4863, A4864, A4865 G:A1299, U:A1300, G:A1635, A:A1637 U:A1300
4qcv A3517 Oph·4Pout G:A1859(OP1) A4638, A4639, A4640, A4641, A4642 G:A1803, A:A1994, A:A1804, G:A1995
4qcv A3535 Oph·4Pout C:A31(OP1) A4686, A4687, A4688, A4689 G:A1285, U:A1244, C:A1245, U:A1286
4qcx A3337 Oph·4Pout G:A741(OP1) A4188, A4189, A4190, A4191 A:A1784, A:A1785, C:A1983, G:A2608 G:A2607
4qcz A3546 Oph·4Pout G:A1859(OP1) A4757, A4758, A4759, A4760, A4761 G:A1803, A:A1994, A:A1804, G:A1995
4qd1 A3454 Oph·4Pout G:A1828(OP1) A4420, A4421, A4422, A4423 G:A1772, A:A1972, A:A1773, G:A1973
4qd1 A3584 Oph·4Pout C:A1636(OP2) A4687, A4688, A4689, A4690, A4691 G:A1299, U:A1300, G:A1635, A:A1637
4qd1 A3282 Oph·4Pout U:A963(OP1) A4026, A4027, A4028, A4029, A4030 C:A964, C:A2498, A:A2497, G:A947
4tol A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A558, G:A557
4ton A1617 Oph·4Pout A:A560(OP2) A1776, A1777, A1778, A1779, A1780 U:A562, A:A563, G:A558, G:A557 A:A559 G:A566
4too A3121 Oph·4Pout U:A2243(OP1) A3733, A3734, A3735, A3736 C:A192, U:A193, C:A198, A:A199
4tou A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4tov A3098 Oph·4Pout U:A1636(OP2) A3650, A3651, A3652, A3653, A3654 G:A1299, A:A1637, A:A1635, G:A1300
4tox A3044 Oph·4Pout G:A1333(OP2) A3388, A3389, A3390, A3391, A3392 U:A1313, C:A1314, G:A1334, G:A1332 G:A1334, C:A1335
4tox A3112 Oph·4Pout C:A31(OP1) A3699, A3700, A3701, A3702, A3703 U:A1199, G:A1239, U:A1240, C:A1200
4tox A3121 Oph·4Pout U:A2243(OP1) A3738, A3739, A3740, A3741 C:A192, U:A193, C:A198, A:A199
4tp0 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tp1 A3112 Oph·4Pout C:A31(OP1) A3703, A3704, A3705, A3706, A3707 C:A1200, G:A1239, U:A1240, U:A1199 A:A1214
4tp2 A1617 Oph·4Pout A:A560(OP2) A1777, A1778, A1779, A1780, A1781 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4tp3 A3043 Oph·4Pout G:A1333(OP2) A3388, A3389, A3390, A3391, A3392 C:A1314, G:A1332, G:A1334, U:A1313 G:A1333, C:A1335
4tp3 A3097 Oph·4Pout U:A1636(OP2) A3642, A3643, A3644, A3645, A3646 A:A1301, A:A1635, A:A1637, G:A1300
4tp4 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tp5 A3111 Oph·4Pout C:A31(OP1) A3705, A3706, A3707, A3708, A3709 C:A1200, G:A1239, U:A1199, U:A1240 A:A1214
4tp7 A3057 Oph·4Pout G:A1828(OP1) A3447, A3448, A3449, A3450, A3451 A:A1773, G:A1972, G:A1973, A:A1772
4tp9 A3112 Oph·4Pout C:A31(OP1) A3701, A3702, A3703, A3704, A3705 C:A1200, G:A1239, U:A1240, U:A1199 A:A1214

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>