Nickel in PDB 6hk5: X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site

The structure of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site, PDB code: 6hk5 was solved by M.Alfano, J.Perard, C.Basset, P.Carpentier, B.Zambelli, J.Timm, S.Crouzy, S.Ciurli, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.800, 74.280, 70.640, 90.00, 92.74, 90.00
R / Rfree (%)	20 / 25.9

The structure of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Nickel atom in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site (pdb code 6hk5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site, PDB code: 6hk5:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:25.2 occ:1.00 NE2 B:HIS26 2.0 26.2 1.0 NE2 C:HIS18 2.1 28.2 1.0 NE2 C:HIS22 2.1 29.2 1.0 NE2 B:HIS22 2.1 37.4 1.0 OE1 G:GLU29 2.2 21.6 1.0 OE2 G:GLU29 2.3 24.9 1.0 CD G:GLU29 2.6 27.3 1.0 CE1 B:HIS26 3.0 34.1 1.0 CD2 B:HIS22 3.0 28.2 1.0 CE1 C:HIS18 3.0 27.6 1.0 CD2 C:HIS22 3.0 27.7 1.0 CD2 B:HIS26 3.1 27.1 1.0 CD2 C:HIS18 3.1 27.4 1.0 CE1 C:HIS22 3.2 32.3 1.0 CE1 B:HIS22 3.2 32.1 1.0 CG G:GLU29 4.1 25.1 1.0 O G:HOH104 4.1 34.6 1.0 ND1 B:HIS26 4.1 35.0 1.0 ND1 C:HIS18 4.1 25.0 1.0 CG B:HIS22 4.2 32.4 1.0 CG B:HIS26 4.2 30.6 1.0 CG C:HIS22 4.2 34.3 1.0 ND1 C:HIS22 4.2 31.1 1.0 ND1 B:HIS22 4.2 36.9 1.0 CG C:HIS18 4.2 27.7 1.0 CB G:GLU29 4.7 28.7 1.0 CA G:GLU29 4.9 27.3 1.0 NE2 G:GLN33 5.0 30.4 1.0

Nickel binding site 2 out of 4 in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni104 b:25.3 occ:1.00 NE2 E:HIS22 2.1 28.4 1.0 NE2 E:HIS26 2.1 24.5 1.0 NE2 G:HIS22 2.1 21.6 1.0 NE2 G:HIS18 2.2 24.2 1.0 OE1 C:GLU29 2.2 22.3 1.0 OE2 C:GLU29 2.4 26.5 1.0 CD C:GLU29 2.6 28.2 1.0 CE1 E:HIS26 3.0 23.3 1.0 CE1 G:HIS22 3.0 30.8 1.0 CE1 E:HIS22 3.1 33.9 1.0 CD2 E:HIS22 3.1 28.9 1.0 CD2 G:HIS18 3.2 25.7 1.0 CD2 E:HIS26 3.2 22.4 1.0 CD2 G:HIS22 3.2 24.0 1.0 CE1 G:HIS18 3.2 27.0 1.0 CG C:GLU29 4.1 28.8 1.0 O C:HOH203 4.2 36.0 1.0 ND1 E:HIS22 4.2 36.5 1.0 ND1 E:HIS26 4.2 24.2 1.0 ND1 G:HIS22 4.2 26.4 1.0 CG E:HIS22 4.2 32.2 1.0 CG E:HIS26 4.3 29.2 1.0 CG G:HIS22 4.3 29.8 1.0 ND1 G:HIS18 4.3 15.3 1.0 CG G:HIS18 4.3 23.6 1.0 NE2 C:GLN33 4.6 49.9 1.0 CB C:GLU29 4.8 23.1 1.0

Nickel binding site 3 out of 4 in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:24.7 occ:1.00 NE2 D:HIS22 2.0 25.4 1.0 NE2 A:HIS26 2.1 28.8 1.0 NE2 D:HIS18 2.1 20.3 1.0 NE2 A:HIS22 2.1 22.9 1.0 OE1 F:GLU29 2.2 22.2 1.0 OE2 F:GLU29 2.4 25.0 1.0 CD F:GLU29 2.6 28.7 1.0 CE1 D:HIS22 2.9 21.7 1.0 CE1 D:HIS18 2.9 25.2 1.0 CD2 A:HIS26 3.0 25.1 1.0 CD2 A:HIS22 3.0 28.2 1.0 CD2 D:HIS22 3.0 23.0 1.0 CE1 A:HIS22 3.1 34.9 1.0 CE1 A:HIS26 3.1 31.3 1.0 CD2 D:HIS18 3.2 23.2 1.0 ND1 D:HIS22 4.0 25.6 1.0 CG F:GLU29 4.1 27.9 1.0 ND1 D:HIS18 4.1 21.6 1.0 ND1 A:HIS22 4.1 29.5 1.0 CG D:HIS22 4.1 28.5 1.0 CG A:HIS22 4.2 33.0 1.0 CG A:HIS26 4.2 32.4 1.0 ND1 A:HIS26 4.2 26.2 1.0 CG D:HIS18 4.3 27.4 1.0 O F:HOH208 4.4 38.0 1.0 NE2 F:GLN33 4.5 44.7 1.0 CB F:GLU29 4.7 23.3 1.0 C4 A:PEG103 4.9 34.2 1.0 C3 A:PEG103 5.0 42.0 1.0

Nickel binding site 4 out of 4 in the X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of X-Ray Structure of A Truncated Mutant of the Metallochaperone Cooj with A High-Affinity Nickel-Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni103 b:26.7 occ:1.00 NE2 H:HIS26 2.1 26.1 1.0 NE2 F:HIS18 2.1 22.4 1.0 NE2 H:HIS22 2.1 26.9 1.0 NE2 F:HIS22 2.1 30.0 1.0 OE1 D:GLU29 2.2 22.5 1.0 OE2 D:GLU29 2.4 21.4 1.0 CD D:GLU29 2.6 28.8 1.0 CE1 H:HIS26 2.9 35.1 1.0 CD2 F:HIS18 3.0 26.7 1.0 CD2 F:HIS22 3.0 29.5 1.0 CE1 H:HIS22 3.0 29.9 1.0 CE1 F:HIS18 3.1 20.8 1.0 CD2 H:HIS22 3.1 33.9 1.0 CE1 F:HIS22 3.1 36.7 1.0 CD2 H:HIS26 3.1 30.2 1.0 ND1 H:HIS26 4.1 38.8 1.0 CG D:GLU29 4.1 23.7 1.0 ND1 F:HIS18 4.2 18.5 1.0 ND1 H:HIS22 4.2 33.4 1.0 CG F:HIS18 4.2 28.8 1.0 CG F:HIS22 4.2 32.5 1.0 ND1 F:HIS22 4.2 28.2 1.0 CG H:HIS26 4.2 37.6 1.0 CG H:HIS22 4.2 29.7 1.0 O D:HOH234 4.7 38.1 1.0 CB D:GLU29 4.7 22.1 1.0 NE2 D:GLN33 4.8 38.1 1.0

M.Alfano, J.Perard, P.Carpentier, C.Basset, B.Zambelli, J.Timm, S.Crouzy, S.Ciurli, C.Cavazza. The Carbon Monoxide Dehydrogenase Accessory Protein Cooj Is A Histidine-Rich Multidomain Dimer Containing An Unexpected Ni(II)-Binding Site. J.Biol.Chem. V. 294 7601 2019.
ISSN: ESSN 1083-351X
PubMed: 30858174
DOI: 10.1074/JBC.RA119.008011