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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 4dv3




4DV3 (3.55Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, c912a, bound with streptomycin
List of all 274 Mg2+ binding sites in the PDB structure 4dv3 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
4dv3 A1740 Or 1  0.03 0  0.55no
4dv3 A1813 Or 1  0.02 0  0.94no
4dv3 A1695 Or 1  0.01 0  0.84no
4dv3 A1817 Or 1  0.03 0  0.99no
4dv3 A1721 Or 1  0.02 0  0.65no
4dv3 A1683 Ob 5  0.65  0.70  0.45no
4dv3 A1749 Ob 1  0.02 0  0.82no
4dv3 A1665 Ob 2  0.16  0.13  1.00no
4dv3 A1722 Ob 1  0.03 0  0.67no
4dv3 A1717 Ob 2  0.06  0.31  0.76no
4dv3 A1642 Ob 1  0.01 0  0.89no
4dv3 A1753 Ob 2  0.04  0.35  0.76no
4dv3 A1762 Ob 1  0.03 0  0.77no
4dv3 A1763 Ob 1  0.01 0  0.87no
4dv3 A1627 Ob 4  0.50  0.72  0.62yes
4dv3 A1688 Ob 4  0.49  0.72  0.89no
4dv3 A1809 Ob 1  0.01 0  0.84no
4dv3 A1697 Ob 2  0.17  0.14  0.77no
4dv3 A1808 Ob 1  0.03 0  0.84no
4dv3 A1655 Ob 1  0.02 0  0.86no

# 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>