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 3ox0 3OX0 (3.05Å) -- RNA : Crystal structure of glycine riboswitch, unbound state List of all 11 Mg2+ binding sites in the PDB structure 3ox0 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 3ox0 B113 Nb G:B62(N7) B136, B137, B138, B139, B140 G:B62, U:B61, C:B39 3ox0 A123 Nb G:A50(N7) A157, A158, A159, A160, A161 G:A49, A:B52 G:A49 3ox0 A125 Nb G:A62(N7) A162, A163, A164, A165, A166 U:A61, C:A39, G:A62 3ox0 B115 Oph·Pout A:B34(OP1) B144, B145, B146, B147, B148 G:B35 G:B36, G:B35 3ox0 A101 Oph·Pout A:A34(OP1) A131, A132, A133, A134, A135 G:A35 G:A35, G:A36 3ox0 A112 Oph·3Pout U:A20(OP2) A152, A153, A154, A155, A156 A:A21, C:A15, G:B25 C:B24 3ox0 B111 cis-2Oph C:B70(OP2), A:B71(OP2) B132, B133, B134, B135 U:B69 G:B72, A:B71 3ox0 A105 cis-2Oph C:A70(OP2), A:A71(OP2) A136, A137, A138, A139 U:A69 G:A72, A:A71 3ox0 B114 cis-2Oph·Or A:B75(OP1), A:B76(OP2) C:B74(O5') B141, B142, B143 C:B74 A:B77, A:B76 3ox0 A110 3Bout A146, A147, A148, A149, A150, A151 G:A25, G:A26, U:A27 3ox0 B124 2Pout·2Bout B149, B150, B151, B152, B153 C:B24, U:B23 G:B25, G:B26

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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