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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 1vq5




1VQ5 (2.6Å) -- RIBOSOME : The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
List of all 118 Mg2+ binding sites in the PDB structure 1vq5 in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
1vq5 08053 Ob 5  0.28  0.97  0.86no
1vq5 08113 Nb 6  0.27  0.93  0.73no
1vq5 08112 Nb 6  0.44  0.92  0.97no
1vq5 08114 Nb 6  0.23  0.86  0.86no
1vq5 08098 Nb 5  0.34  0.82  0.88no
1vq5 08046 Nb 4  0.33  0.60  0.99no
1vq5 08024 Nb 4  0.35  0.49  0.66no
1vq5 08111 Nb 6  0.38  0.93  0.95no
1vq5 08075 2Or 6  0.55  0.87  0.84yes
1vq5 08099 2Or 5  0.27  0.77  0.94no
1vq5 08097 2Ob 6  0.32  0.84  0.94no
1vq5 08042 2Ob 6  0.27  0.72  0.94no
1vq5 08102 Ob·Nb 5  0.35  0.76  0.92no
1vq5 08011 2Nb 6  0.86  0.94  0.54yes
1vq5 08117 2Or·Nb 5  0.23  0.68  1.00no
1vq5 08050 Oph 2  0.27  0.23  0.69no
1vq5 08019 Oph·Pout 6  0.65  0.80  0.72yes
1vq5 08092 Oph·Pout 4  0.37  0.66  0.59no
1vq5 08082 Oph·Pout 4  0.28  0.41  0.75no
1vq5 08084 Oph·Pout 6  0.74  0.96  0.98yes

# Validation parameters Qv, Qs, Qe are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Qv measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg2+ (+2)
Qs measures the geometrical symmetry of the ligands distribution around the Mg2+ required for octahedral geometry
Qe measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg2+ compared to those of all atoms in its environment

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>