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

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List of Mg2+ binding sites in structure 1kd1




1KD1 (3Å) -- RIBOSOME : Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
List of all 44 Mg2+ binding sites in the PDB structure 1kd1 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
1kd1 A8058 poly-nuclear Mg2+ site G:A2013(OP2) A3760, A7821, A7822, A7888, C8634 G:A1884, U:A1883, C:A2626
1kd1 A8031 poly-nuclear Mg2+ site U:A777(OP2), C:A778(OP2) A3273, A7801, A7802, A7803 U:A864
1kd1 A8096 poly-nuclear Mg2+ site G:A1848(O6), G:A1849(O6) A3659, A3696, A3829 A:A1847 U:A1883
1kd1 A8059 poly-nuclear Mg2+ site G:A2618(OP1) A3717, A4043, A7773, A9036, A9040 G:A2642, U:A2619, C:A2641 G:A2642, G:A2643

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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