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 1egk 1EGK (3.1Å) -- DNA-RNA HYBRID : Crystal structure of a nucleic acid four-way junction List of all 13 Mg2+ binding sites in the PDB structure 1egk 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 1egk C14 Bout C93, C94, C95, C96, C97, C98 G:C118 1egk C6 Bout C45, C46, C47, C48, C49, C50 G:C113 1egk A23 2Bout A34, A35, A36, A37, A38, A39 C:A17, G:A18 1egk A26 2Bout A49, A50, A51, A52, A53, A54 U:A15, G:A16 1egk A21 2Bout A28, A29, A30, A31, A32, A33 G:A2, G:A3 1egk A27 2Bout A55, A56, A57, A58, A59, A60 G:A13, G:A12 1egk A22 2Bout B55, B56, B57, B58, B59, B60 G:A9, DG:B31 1egk C4 2Bout B62, B63, C34, C35, C36, C37 G:C103, G:C102 1egk C13 4Bout C87, C88, C90, C91, C92, D89 U:C115, G:C116, DA:D126, DG:D124 1egk C3 Pout·2Bout B61, C28, C29, C30, C31, C32 DA:B45 A:C104, G:C105 1egk A25 Pout·3Bout A46, A47, A48, B65, B66, D70 G:A3 DG:B32, DG:D136, DA:D135 1egk C9 Pout·3Bout B64, C64, C65, C67, C68, D63 G:C103 DG:B36, DA:B45, DG:D132 1egk A24 2Pout·Bout A40, A41, A42, A43, A44, A45 A:A19, DC:D153 A:A19

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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