MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A3000, See in JSmolClick on the image to toggle views Site type: Oph·5Pout Schematic drawing for Oph·5Pout List of all 37 Mg2+ binding sites with the site type Oph·5Pout 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 1 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofz A2997 Oph·5Pout U:A1636(OP2) A3477, A3478, A3479, A3480, A3481 A:A1637, A:A1301, A:A1635, G:A1299, G:A1300 3ofc A2998 Oph·5Pout U:A1636(OP2) A3488, A3489, A3490, A3491, A3492 G:A1300, A:A1637, A:A1301, A:A1635, G:A1299 3r8t A2999 Oph·5Pout U:A1636(OP2) A3521, A3522, A3523, A3524, A3525 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300 3i1r A3000 Oph·5Pout U:A1636(OP2) A3494, A3495, A3496, A3497, A3498 A:A1301, G:A1300, A:A1637, A:A1635, G:A1299 3r8s A3000 Oph·5Pout U:A1636(OP2) A3550, A3551, A3552, A3553, A3554 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300 3i20 A3000 Oph·5Pout U:A1636(OP2) A3494, A3495, A3496, A3497, A3498 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300 4pec A3096 Oph·5Pout U:A1636(OP2) A3643, A3644, A3645, A3646, A3647 A:A1301, A:A1637, G:A1299, A:A1635, G:A1300 4too A3097 Oph·5Pout U:A1636(OP2) A3641, A3642, A3643, A3644, A3645 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 4tpb A3097 Oph·5Pout U:A1636(OP2) A3642, A3643, A3644, A3645, A3646 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 4tpd A3097 Oph·5Pout U:A1636(OP2) A3652, A3653, A3654, A3655, A3656 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 4tp7 A3098 Oph·5Pout U:A1636(OP2) A3642, A3643, A3644, A3645, A3646 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 4tpf A3098 Oph·5Pout U:A1636(OP2) A3645, A3646, A3647, A3648, A3649 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 4tox A3098 Oph·5Pout U:A1636(OP2) A3646, A3647, A3648, A3649, A3650 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300 3v2f A3235 Oph·5Pout C:A1636(OP2) A4047, A4048, A4049, A4050, A4051 G:A1299, U:A1300, G:A1635, A:A1301, A:A1637 3v25 A3286 Oph·5Pout C:A1636(OP2) A3698, A3699, A3700, A3701, A3702 G:A1299, U:A1300, G:A1635, A:A1301, A:A1637 4nw1 A3551 Oph·5Pout C:A1636(OP2) A4710, A4711, A4712, A4713 G:A1299, U:A1300, A:A1301, G:A1635, A:A1637 4qcx A3555 Oph·5Pout C:A1636(OP2) A4628, A4629, A4630, A4631 G:A1299, A:A1301, U:A1300, G:A1635, A:A1637 4nvx A3557 Oph·5Pout C:A1636(OP2) A4711, A4712, A4713, A4714 G:A1299, U:A1300, G:A1635, A:A1301, A:A1637 1yjw 78035 Oph·5Pout G:01484(OP2) 07233, 07235, 07237, 07289, 07290 C:01455, C:01456, U:01457, A:01485, C:01483 U:01457, G:01484 1nji A8060 Oph·5Pout G:A175(OP2) A7818, A7819, A7820, A9167 C:A173, G:A225, U:A172, G:A393, U:A392 1jj2 08060 Oph·5Pout G:0175(OP2) 07373, 07374, 07375, 08687 C:0173, G:0225, U:0172, G:0393, U:0392 1k9m A8060 Oph·5Pout G:A175(OP2) A7836, A7837, A7838, A9172 C:A173, G:A225, U:A172, G:A393, U:A392 2otj 08060 Oph·5Pout G:0175(OP2) 07820, 07821, 07822, 09172 C:0173, G:0225, U:0172, G:0393, U:0392 1s72 08060 Oph·5Pout G:0175(OP2) 07328, 07329, 07330, 08687 C:0173, G:0225, U:0172, G:0393, U:0392 3cc2 08060 Oph·5Pout G:0175(OP2) 07386, 07387, 07388, 08694 C:0173, G:0225, U:0172, G:0393, U:0392

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>