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 2nug 2NUG (1.7Å) -- HYDROLASE/RNA : Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 1.7-angstrom resolution List of all 13 Mg2+ binding sites in the PDB structure 2nug 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 2nug E505 cis-2Oph A:E17(OP2), G:E18(OP2) E509, E510, E511, E512 2nug F511 cis-2Oph A:F17(OP2), G:F18(OP2) F517, F518, F519, F520 2nug D516 3Bout E513, E526, D522, D531, D535, D562 G:D12, C:D11, A:E17 2nug C515 3Bout C535, C538, C559, C563 G:C4, G:C5, U:C6 2nug D514 3Bout D529, D533, D550, D551, D552 G:D4, G:D5, U:D6 2nug C519 3Bout C526, C530, C540, C546, C562, F551 G:C12, C:C11, A:F17 2nug F513 4Bout E522, F542, F543, F544, F545, F552 G:E26, G:F26, U:E25, U:F25 2nug A506 Pout C520, C521, A526, A527, A528, A529 C:C7 2nug B512 Pout D518, D519, D563, B527, B528, B529 C:D7 2nug B510 Mg2+ bound by non-RNA F516, A530, B525, B526 GLU:B37(OE1), GLU:B40(OE1) A:F17, G:F18 2nug A504 Mg2+ bound by non-RNA E508, A524, A525, B519 GLU:A37(OE1), GLU:A40(OE1) G:E18 2nug A501 poly-nuclear Mg2+ site G:D12(O3') D517, A518, A519 ASP:A44(OD1), GLU:A110(OE2) A:E17 2nug B507 poly-nuclear Mg2+ site G:C12(O3') C522, C523, B520 ASP:B44(OD1), GLU:B110(OE2) A:F17

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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