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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 1vs8



1VS8 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is
List of all 104 Mg2+ binding sites in the PDB structure 1vs8 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
1vs8 B2935 4Pout·Rout B3165, B3166, B3167, B3168, B3169, B3170 U:B2017, G:B579, U:B2016, G:B578 U:B1255
1vs8 B2966 4Pout·Rout B3315, B3316, B3317, B3318, B3319, B3320 G:B559, A:B1008, G:B2038, C:B560 C:B1007
1vs8 B2910 4Pout·Bout B3041, B3042, B3043, B3044, B3045, B3046 C:B1986, A:B1669, A:B1987, C:B2551 G:B1954
1vs8 B2909 4Pout·Bout B3035, B3036, B3037, B3038, B3039, B3040 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959

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].

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>