MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 4enb 4ENB (2.3Å) -- RNA : Crystal structure of fluoride riboswitch, bound to iridium List of all 4 Mg2+ binding sites in the PDB structure 4enb in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4enb A111 Oph·Pout A:A40(OP2) A214, A221, A223, A224, A225 G:A39 A:A40 U:A7, A:A49, C:A50 4enb A110 poly-nuclear Mg2+ site U:A7(OP1), G:A8(OP2) A226, A232, A235 F:A106(F) U:A41 4enb A112 poly-nuclear Mg2+ site A:A6(OP2), U:A7(OP2), U:A41(OP1), G:A42(OP2) A222 F:A106(F) 4enb A113 poly-nuclear Mg2+ site A:A6(OP1), G:A42(OP1) A226, A233, A234 F:A106(F) G:A5

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>