Nickel 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:

Cadmium	(Cd)	1 atom
Cobalt	(Co)	2 atoms
Magnesium	(Mg)	1 atom

The binding sites of Nickel 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 Nickel atom.
In total 3 binding sites of Nickel where 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:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 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 Nickel with other atoms in the Ni 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:Ni403 b:31.6 occ:0.80 O A:HOH742 2.2 54.1 1.0 O A:HOH743 2.2 43.3 1.0 ND1 A:HIS304 2.4 26.1 1.0 O A:HOH756 2.6 56.3 1.0 CE1 A:HIS304 3.2 27.1 1.0 CG A:HIS304 3.5 24.9 1.0 CB A:HIS304 3.9 23.2 1.0 O A:HOH745 4.0 44.5 1.0 O A:HOH682 4.1 36.7 1.0 CA A:HIS304 4.3 23.3 1.0 NE2 A:HIS304 4.4 26.8 1.0 CD2 A:HIS304 4.6 25.8 1.0 CB A:PRO85 4.8 32.3 1.0

Nickel binding site 2 out of 3 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 Nickel with other atoms in the Ni binding site number 2 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:Ni404 b:44.3 occ:0.50 NE2 A:HIS103 2.5 35.7 1.0 CD2 A:HIS103 3.3 32.2 1.0 CE1 A:HIS103 3.6 35.0 1.0 O A:HOH677 4.1 48.6 1.0 CG A:HIS103 4.6 30.6 1.0 ND1 A:HIS103 4.7 34.3 1.0 CG A:LYS130 5.0 33.0 1.0 O A:HOH648 5.0 44.0 1.0

Nickel binding site 3 out of 3 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 Nickel with other atoms in the Ni binding site number 3 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:Ni405 b:59.5 occ:0.50 NE2 A:HIS288 2.6 27.3 1.0 CE1 A:HIS288 2.6 28.3 1.0 O A:HOH713 3.6 51.4 1.0 O A:HOH639 3.8 37.7 1.0 ND1 A:HIS288 3.9 27.1 1.0 CD2 A:HIS288 4.0 25.6 1.0 CG A:HIS288 4.6 24.4 1.0 OG1 A:THR292 4.7 21.0 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