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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 1k73




1K73 (3.01Å) -- RIBOSOME : Co-crystal structure of anisomycin bound to the 50s ribosomal subunit
List of all 117 Mg2+ binding sites in the PDB structure 1k73 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
1k73 A8099 Or 4  0.31  0.63  0.95no
1k73 A8053 Ob 6  0.45  0.85  0.97no
1k73 A8098 Nb 6  0.42  0.87  0.48no
1k73 A8024 Nb 5  0.28  0.60  0.55no
1k73 A8111 Nb 6  0.53  0.79  0.68yes
1k73 A8112 Nb 6  0.48  0.94  0.83no
1k73 A8046 Nb 4  0.37  0.55  0.83no
1k73 A8114 Nb 6  0.29  0.87  0.69no
1k73 A8075 2Or 6  0.49  0.60  0.60no
1k73 A8042 2Ob 6  0.35  0.86  0.84no
1k73 A8097 2Ob 6  0.44  0.73  0.87no
1k73 A8102 Ob·Nb 6  0.30  0.78  0.91no
1k73 A8011 2Nb 6  0.22  0.84  0.86no
1k73 A8117 2Or·Nb 6  0.35  0.71  0.75no
1k73 A8039 Oph·Pout 6  0.86  0.87  0.82yes
1k73 A8050 Oph·Pout 2  0.11  0.19  0.70no
1k73 A8090 Oph·Pout 3  0.17  0.25  0.65no
1k73 A8051 Oph·Pout 4  0.50  0.57  0.62no
1k73 A8084 Oph·Pout 6  0.51  0.75  0.53yes
1k73 A8047 Oph·Pout 4  0.56  0.53  0.73no

# 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>