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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 4ji2




4JI2 (3.64Å) -- RIBOSOME : Crystal structure of 30s ribosomal subunit from thermus thermophilus
List of all 283 Mg2+ binding sites in the PDB structure 4ji2 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
4ji2 A1717 Or 1  0.05 0  0.56no
4ji2 A1817 Or 1  0.02 0  0.80no
4ji2 A1626 Or 3  0.33  0.38  0.60no
4ji2 A1742 Or 1  0.03 0  0.82no
4ji2 A1747 Or 2  0.11  0.13  0.53no
4ji2 A1729 Or 1  0.03 0  0.84no
4ji2 A1662 Ob 1  0.02 0  0.81no
4ji2 A1642 Ob 1  0.03 0  0.72no
4ji2 A1796 Ob 1  0.01 0  0.87no
4ji2 A1619 Ob 1  0.02 0  0.87no
4ji2 A1783 Ob 1  0.05 0  0.90no
4ji2 A1660 Ob 3  0.34  0.39  0.94no
4ji2 A1605 Ob 1  0.01 0  0.78no
4ji2 A1731 Ob 1  0.01 0  0.94no
4ji2 A1748 Ob 1  0.01 0  0.86no
4ji2 A1743 Ob 1  0.01 0  0.81no
4ji2 A1735 Ob 1  0.02 0  0.86no
4ji2 A1749 Ob 1  0.03 0  0.88no
4ji2 A1854 Ob 1  0.03 0  0.85no
4ji2 A1842 Ob 1  0.02 0  0.90no

# 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>