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 3q3z 3Q3Z (2.51Å) -- RNA : Structure of a c-di-gmp-ii riboswitch from c. acetobutylicum bound to c-di-gmp List of all 12 Mg2+ binding sites in the PDB structure 3q3z 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 3q3z A85 Oph·2Pout A:A34(OP1) V177, A162, A163, A164, A165 G:V46, A:A33 3q3z A86 Oph·Nb G:A67(OP2) A:A61(N7) A166, A168, A170 A:A61 U:A66 G:A62 3q3z A3 Oph·Nb G:A56(OP1) G:A38(N7) A91, A92, A94, A132 G:A56, G:A38 U:A37 G:A39, A:A70 3q3z V82 Oph·Nb G:V56(OP1) G:V38(N7) V88, V90, V93, V94 G:V38 U:V37 G:V38, G:V39, A:V70 3q3z V85 cis-2Oph G:V46(OP1), A:A34(OP2) V175, V176, A160, A161 3q3z V87 cis-2Oph A:V34(OP2), G:A46(OP2) V178, V179, V180, A169 A:V33 3q3z V83 trans-2Oph U:V60(OP1), U:V66(OP1) V171, V172, V173, V174 A:V61 3q3z A6 trans-2Oph U:A60(OP1), U:A66(OP1) A95, A96, A101, A102 A:A61 3q3z V4 cis-2Oph·Ob A:V61(OP1), G:V62(OP2) U:V63(O4) V97, V98, V99 3q3z A82 cis-2Oph·Ob A:A61(OP1), G:A62(OP2) U:A63(O4) A87, A89, A90 3q3z A83 2Pout·3Bout A103, A105, A106, A113, A115, A116 G:A73, C:A72 G:A12, A:A74, G:A73 3q3z V5 2Pout·4Bout V100, V104, V107, V108, V109, V110 C:V72, G:V73 G:V12, A:V74, A:V13, G:V73

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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