MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4n:B3007, See in JSmolClick on the image to toggle views Site type: cis-2Oph·Or Schematic drawing for cis-2Oph·Or List of all 36 Mg2+ binding sites with the site type cis-2Oph·Or 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 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 3owi A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A136, A137, A138 U:A69 3owi B114 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B150, B151, B152 U:B69, U:B67 3oww B114 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B149, B150, B151 U:B69, U:B67 3oww A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A135, A136, A137 U:A67, U:A69 3ox0 B114 cis-2Oph·Or A:B75(OP1), A:B76(OP2) C:B74(O5') B141, B142, B143 C:B74 A:B77, A:B76 3oxj B111 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B135, B136, B137 U:B69, U:B67 3oxj A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A129, A130, A131 U:A69 3oxm A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A115, A141, A142 C:A68, U:A69 3oxm B111 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B109, B117, B118 C:B68, U:B69, U:B67 4dr2 A1746 cis-2Oph·Or G:A1197(OP1), G:A1198(OP2) C:A1054(O5') A2369, A2370, A2371 U:A1196 4kj5 A3101 cis-2Oph·Or A:A2448(OP2), C:A2498(OP2) A:A2497(O2') A3677, A3679 C:A2499

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>