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Center for Structural Genomics of Infectious Diseases

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Mg2+ site A1966 in 3I9B (3.5Å) -- RIBOSOME : Initiation complex of 70s ribosome with two trnas and mrna. this entry 3i9b contains 30s ribosomal subunit of molecule b. the 50s ribosomal subunit can be found in pdb entry 3i9c. molecule a in the same asymmetric unit is deposited as 3i9d (30s) and 3i9e

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Binding environment of Mg2+ A1966

Site type*

mer-3Oph·Or

Inner
sphere		 Oph C:A1054(OP1), G:A1197(OP1), G:A1198(OP2)
Or
Ob+Nb
Water
Other
Outer
sphere		 Pout
Rout
Bout
Each outer-sphere moiety is listed only once and only if it does not form inner-sphere interaction
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Inner-sphere Residue Name:
Outer-sphere Moiety Name:
Metal Distances:
Outer-sphere Distances:
B factor(Occupancy):
Nucleic Acid Cartoon:
Spin:
Antialiasing:		 On Off
On Off
On Off
On Off
On Off
On Off
On Off
On Off

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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