Calcium in PDB 3omj: Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding

The structure of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding, PDB code: 3omj was solved by D.M.Chenoweth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.44 / 0.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	39.831, 39.831, 84.567, 90.00, 90.00, 90.00
R / Rfree (%)	11.2 / 12.4

The structure of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Calcium atom in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding (pdb code 3omj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding, PDB code: 3omj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:7.4 occ:1.00 O A:HOH247 2.4 9.6 1.0 O A:HOH246 2.4 9.5 1.0 O A:HOH253 2.4 7.9 1.0 O A:HOH124 2.4 9.4 1.0 O A:HOH252 2.4 13.4 1.0 O B:HOH125 2.4 10.9 1.0 O B:HOH245 2.4 11.6 1.0 O A:HOH248 4.3 14.9 1.0 O B:HOH139 4.4 17.7 1.0 O B:HOH254 4.4 5.6 0.5 O A:HOH123 4.4 7.7 1.0 O B:HOH12 4.6 8.4 1.0 O A:HOH128 4.6 11.2 1.0 O B:HOH11 4.6 15.2 0.5 N7 A:DA3 4.7 6.0 1.0 O B:HOH131 4.8 13.2 1.0 O A:HOH241 4.8 21.6 1.0 O A:HOH88 4.8 25.4 1.0 I A:C382 4.9 7.1 1.0

Calcium binding site 2 out of 4 in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:19.1 occ:0.50 CA A:CA301 1.2 6.5 0.5 O A:HOH161 1.2 14.6 0.5 O A:HOH161 2.2 14.2 0.5 O A:HOH32 2.3 9.8 1.0 O A:HOH34 2.5 9.2 1.0 O A:HOH74 2.7 20.1 0.5 O A:HOH133 2.7 21.4 1.0 O A:HOH73 2.8 13.8 0.5 O A:HOH218 3.5 20.2 1.0 O A:HOH41 3.7 10.9 1.0 O A:HOH211 3.7 44.1 1.0 O A:HOH51 4.3 16.0 1.0 OP2 A:DT8 4.7 9.6 0.6 OP2 A:DT8 4.8 7.4 0.4 OP1 A:DC7 5.0 5.2 1.0

Calcium binding site 3 out of 4 in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:6.5 occ:0.50 CA A:CA300 1.2 19.1 0.5 O A:HOH74 1.8 20.1 0.5 O A:HOH34 2.2 9.2 1.0 O A:HOH133 2.3 21.4 1.0 O A:HOH32 2.3 9.8 1.0 O A:HOH73 2.4 13.8 0.5 O A:HOH161 2.4 14.6 0.5 O A:HOH41 2.5 10.9 1.0 O A:HOH161 3.0 14.2 0.5 OP1 A:DC7 4.2 5.2 1.0 O A:HOH218 4.3 20.2 1.0 O A:HOH51 4.5 16.0 1.0 OP2 A:DC7 4.6 5.7 1.0 OP2 A:DT8 4.6 7.4 0.4 O A:HOH22 4.6 9.0 1.0 O A:HOH211 4.7 44.1 1.0 P A:DC7 4.8 4.8 1.0 OP2 A:DT8 4.8 9.6 0.6 O5' A:DC7 4.9 4.7 1.0

Calcium binding site 4 out of 4 in the Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:19.9 occ:0.50 O B:HOH45 2.3 17.6 1.0 O1P B:C382 2.3 9.5 1.0 O B:HOH85 2.4 27.8 1.0 P B:C382 3.7 8.4 1.0 O B:HOH44 4.0 14.8 1.0 O5' B:C382 4.3 8.5 1.0 O2P B:C382 4.4 9.3 1.0 C5' B:C382 4.4 9.2 1.0 O B:HOH80 4.6 20.2 1.0 O3' B:DC1 4.7 8.8 1.0

D.M.Chenoweth, P.B.Dervan. Structural Basis For Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding. J.Am.Chem.Soc. V. 132 14521 2010.
ISSN: ISSN 0002-7863
PubMed: 20812704
DOI: 10.1021/JA105068B