Cadmium in PDB 4oqp: Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate

The structure of Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate, PDB code: 4oqp was solved by P.Rezacova, J.Skerlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.995, 78.983, 91.338, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.1

The structure of Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Cobalt	(Co)	2 atoms
Magnesium	(Mg)	1 atom

The binding sites of Cadmium atom in the Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate (pdb code 4oqp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate, PDB code: 4oqp:

Cadmium binding site 1 out of 1 in the Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis in Complex with Deoxyribose-5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:17.5 occ:1.00 ND1 A:HIS191 2.3 20.2 1.0 O A:HOH700 2.3 20.2 1.0 OD2 A:ASP189 2.4 17.5 1.0 O A:HOH540 2.4 19.0 1.0 OD1 A:ASP189 2.4 17.6 1.0 CG A:ASP189 2.7 17.2 1.0 CE1 A:HIS191 3.2 22.1 1.0 CG A:HIS191 3.3 19.9 1.0 CB A:HIS191 3.5 18.5 1.0 CB A:ASP189 4.2 16.4 1.0 N A:HIS191 4.3 18.7 1.0 NE2 A:HIS191 4.3 22.9 1.0 CD2 A:HIS191 4.4 21.5 1.0 CA A:HIS191 4.6 18.0 1.0 O A:HOH597 4.7 26.0 1.0 N A:ARG190 5.0 19.4 1.0

J.Skerlova, M.Fabry, M.Hubalek, Z.Otwinowski, P.Rezacova. Structure of the Effector-Binding Domain of Deoxyribonucleoside Regulator Deor From Bacillus Subtilis. Febs J. V. 281 4280 2014.
ISSN: ISSN 1742-464X
PubMed: 24863636
DOI: 10.1111/FEBS.12856