MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 3zgz

3ZGZ (2.4Å) -- LIGASE/RNA : Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and toxic moiety from agrocin 84 (tm84) in aminoacylation- like conformation
List of all 4 Mg2+ binding sites in the PDB structure 3zgz 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
3zgz B1078 Ob·Nb G:B45(O6) B2063, B2064, B2065, B2066 G:B45 G:B46, G:B21
3zgz B1077 Oph·2Pout U:B20(OP2) B2058, B2059, B2060, B2061, B2062 G:B59, A:B20 A:B20 U:B60, U:B48, G:B59
3zgz B1080 Oph·2Pout U:B8(OP1) B2071, B2072, B2073, B2074, B2075 G:B12, G:B13 G:B13
3zgz B1079 cis-2Oph U:B8(OP2), G:B9(OP2) B2067, B2068, B2069, B2070 U:B11, G:B12

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>