Nickel in PDB 4oeu: Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His)

The structure of Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His), PDB code: 4oeu was solved by H.Lebrette, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.63 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.480, 72.770, 86.090, 90.00, 111.99, 90.00
R / Rfree (%)	19.2 / 24.1

The structure of Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His) (pdb code 4oeu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His), PDB code: 4oeu:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:28.9 occ:1.00 N A:HIS502 1.9 25.8 1.0 NE2 A:HIS26 2.0 30.2 1.0 NE2 A:HIS480 2.1 30.3 1.0 ND1 A:HIS502 2.1 29.9 1.0 NE2 A:HIS481 2.2 31.8 1.0 O A:HIS502 2.2 27.9 1.0 CA A:HIS502 2.8 26.8 1.0 C A:HIS502 2.8 27.9 1.0 CD2 A:HIS480 3.0 31.0 1.0 CD2 A:HIS26 3.0 30.6 1.0 CD2 A:HIS481 3.0 32.3 1.0 CE1 A:HIS26 3.1 30.5 1.0 CE1 A:HIS502 3.1 31.3 1.0 CG A:HIS502 3.1 28.4 1.0 CE1 A:HIS480 3.1 31.9 1.0 CE1 A:HIS481 3.3 32.3 1.0 CB A:HIS502 3.4 27.3 1.0 OXT A:HIS502 4.0 28.1 1.0 CG A:HIS480 4.1 32.4 1.0 O A:GLY383 4.1 30.9 1.0 CG A:HIS26 4.1 32.0 1.0 ND1 A:HIS26 4.1 31.0 1.0 ND1 A:HIS480 4.2 33.2 1.0 NE2 A:HIS502 4.2 31.9 1.0 CD2 A:HIS502 4.2 30.0 1.0 CG A:HIS481 4.2 33.5 1.0 ND1 A:HIS481 4.3 33.6 1.0 NH1 A:ARG344 4.5 39.1 1.0 O2 A:PEG505 5.0 49.4 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:32.4 occ:1.00 N B:HIS502 1.9 32.3 1.0 ND1 B:HIS502 2.0 42.5 1.0 NE2 B:HIS480 2.1 38.3 1.0 NE2 B:HIS26 2.1 32.1 1.0 NE2 B:HIS481 2.2 41.5 1.0 O B:HIS502 2.3 29.6 1.0 CA B:HIS502 2.7 32.8 1.0 C B:HIS502 2.8 31.5 1.0 CG B:HIS502 3.0 40.5 1.0 CD2 B:HIS480 3.0 37.5 1.0 CD2 B:HIS481 3.0 40.9 1.0 CE1 B:HIS502 3.0 43.4 1.0 CD2 B:HIS26 3.0 35.8 1.0 CE1 B:HIS26 3.1 32.3 1.0 CE1 B:HIS480 3.1 37.1 1.0 CB B:HIS502 3.3 35.8 1.0 CE1 B:HIS481 3.3 42.5 1.0 OXT B:HIS502 4.0 31.1 1.0 NE2 B:HIS502 4.1 43.8 1.0 CD2 B:HIS502 4.1 42.9 1.0 CG B:HIS480 4.1 36.6 1.0 ND1 B:HIS480 4.1 37.2 1.0 ND1 B:HIS26 4.1 31.7 1.0 CG B:HIS26 4.2 35.3 1.0 O B:GLY383 4.2 25.9 1.0 CG B:HIS481 4.2 41.4 1.0 ND1 B:HIS481 4.3 43.0 1.0 NH1 B:ARG344 4.4 39.2 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Nikz From Campylobacter Jejuni in Complex with Ni(L-His) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni503 b:39.6 occ:0.45 NE2 B:HIS417 2.1 44.4 1.0 O B:HOH768 2.2 60.7 1.0 O B:HOH714 2.2 32.4 1.0 CD2 B:HIS417 3.1 40.3 1.0 CE1 B:HIS417 3.1 44.7 1.0 OG B:SER400 4.2 38.0 1.0 ND1 B:HIS417 4.2 42.0 1.0 CG B:HIS417 4.2 39.0 1.0 CB B:SER400 4.9 35.5 1.0 OD2 B:ASP422 5.0 40.4 1.0

H.Lebrette, C.Brochier-Armanet, B.Zambelli, H.De Reuse, E.Borezee-Durant, S.Ciurli, C.Cavazza. Promiscuous Nickel Import in Human Pathogens: Structure, Thermodynamics, and Evolution of Extracytoplasmic Nickel-Binding Proteins. Structure 2014.
ISSN: ISSN 0969-2126
PubMed: 25199691
DOI: 10.1016/J.STR.2014.07.012