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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 3oww



3OWW (2.8Å) -- RNA : Crystal structure of the glycine riboswitch bound to glycine
List of all 17 Mg2+ binding sites in the PDB structure 3oww 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3oww A119 Nb G:A62(N7) A182, A183, A184, A185, A186 G:A62, C:A39, U:A61
3oww A120 Oph·Pout A:A21(OP2) A187, A188, A189, A190, A191 A:A51 U:A19 A:A21, A:A22, U:A23, A:B53
3oww B121 Oph·Pout A:B52(OP2) B162, B163, B164, B165, B166 A:B51 A:B52, G:B49
3oww B118 Oph·Pout A:B78(OP2) B157, B158, B159, B160, B161 A:B77 G:B79, G:B80, A:B78
3oww A116 Oph·Pout A:A78(OP2) A177, A178, A179, A180, A181 A:A77 A:A78, G:A79, G:A80
3oww B117 Oph·Pout U:B23(OP1) B152, B153, B154, B155, B156 C:B24 G:B26, G:B25
3oww A111 Oph·3Pout U:A20(OP2) A167, A168, A169, A170, A171 A:A21, C:A15, G:B25 C:B24
3oww B113 cis-2Oph A:B34(OP1), G:B35(OP2) B145, B146, B147, B148 A:B81 G:B35, G:B36
3oww A105 cis-2Oph C:A70(OP2), A:A71(OP2) A145, A146, A147, A148 U:A69 G:A72, A:A71
3oww A101 cis-2Oph A:A34(OP1), G:A35(OP2) A131, A132, A133, A134 A:A81 G:A35, G:A36
3oww A104 cis-2Oph A:A75(OP1), A:A76(OP2) A142, A143, A144 C:A74 A:A76, A:A77
3oww A103 trans-2Oph A:A22(OP1), A:A75(OP2) A138, A139, A140, A141 C:A74 A:A75
3oww A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A135, A136, A137 U:A67, U:A69
3oww B114 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B149, B150, B151 U:B69, U:B67
3oww B122 mer-3Oph C:B74(OP1), A:B75(OP1), A:B76(OP2) B167, B168, B169 A:B76, A:B77, A:B78
3oww A107 3Pout A149, A150, A151, A152, A153, B134 G:A32, U:A67, G:B10
3oww B108 4Pout A154, B135, B136, B137, B138, B139 G:A10, U:B67, G:B32, C:B68

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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