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 3ivk 3IVK (3.1Å) -- IMMUNE SYSTEM / RNA : Crystal structure of the catalytic core of an rna polymerase ribozyme complexed with an antigen binding antibody fragment List of all 16 Mg2+ binding sites in the PDB structure 3ivk 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 3ivk M128 Nb G:M2(N7) M165, M166, M167, M168, M169 U:M8 G:M1 3ivk C128 Nb G:C2(N7) C166, C167, C168, C169, C170 U:C8 G:C1 3ivk C123 2Bout C144, C145, C146, C147, C148, C149 G:C87, G:C88 3ivk M123 2Bout M144, M145, M146, M147, M148, M149 G:M87, G:M88 3ivk M129 3Bout M170, M171, M172, M173, M174, M175 G:M17, G:M18, U:M16 3ivk C124 3Bout C150, C151, C152, C153, C154, C155 G:C72, A:C73, G:C105 3ivk M125 3Bout M156, M157, M158, M159, M160, M161 A:M80, G:M81, G:M75 3ivk M124 3Bout M150, M151, M152, M153, M154, M155 G:M72, A:M73, G:M105 3ivk C125 3Bout C156, C157, C158, C159, C160, C161 A:C80, G:C81, G:C75 3ivk C129 3Bout C171, C172, C173, C174, C175, C176 G:C17, G:C18, U:C16 3ivk C122 4Bout C138, C139, C140, C141, C142, C143 A:C97, G:C91, G:C92, U:C93 3ivk M134 5Bout M182, M183, M184, M185, M186, M187 G:M77, U:M36, G:M37, C:M38, G:M78 3ivk C134 5Bout C183, C184, C185, C186, C187, C188 G:C77, U:C36, G:C37, C:C38, G:C78 3ivk M122 5Bout M138, M139, M140, M141, M142, M143 A:M97, G:M91, G:M92, U:M93, U:M94 3ivk M132 Pout·3Bout M176, M177, M178, M179, M180, M181 A:M-4 A:M-4, G:M-3, U:M-2 3ivk C132 Pout·4Bout C177, C178, C179, C180, C181, C182 A:C-4 A:C-4, A:C14, G:C-3, U:C-2

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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