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 3oxb 3OXB (2.95Å) -- RNA : Crystal structure of glycine riboswitch with single mutation List of all 6 Mg2+ binding sites in the PDB structure 3oxb 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 3oxb B112 Nb G:B62(N7) B131, B132, B133, B134, B135 C:B39, G:B62, A:B63 3oxb A131 Nb G:A50(N7) A154, A155, A156, A157, A158 G:A49, A:B52 G:A49 3oxb A101 Oph·Pout A:A34(OP1) A132, A133, A134, A135, A136 G:A35 G:A35, G:A36 3oxb B129 Oph·Pout A:B34(OP1) B136, B137, B138, B139, B140 G:B35 G:B35, G:B36 3oxb B130 Oph·2Pout U:B23(OP1) B141, B142, B143, B144, B145 C:B24, G:B25 G:B26, G:B25 3oxb A111 3Pout·2Rout A149, A150, A151, A152, A153 A:A21, U:A20, C:A15 A:A13, C:B24

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].

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