Nickel in PDB 6g1b: Corynebacterium Glutamicum Oxyr, Oxidized Form

The structure of Corynebacterium Glutamicum Oxyr, Oxidized Form, PDB code: 6g1b was solved by D.R.Young, B.P.Pedre, J.M.Messens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.05 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.307, 46.186, 116.692, 90.00, 121.92, 90.00
R / Rfree (%)	19.6 / 23

The structure of Corynebacterium Glutamicum Oxyr, Oxidized Form also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Nickel atom in the Corynebacterium Glutamicum Oxyr, Oxidized Form (pdb code 6g1b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Corynebacterium Glutamicum Oxyr, Oxidized Form, PDB code: 6g1b:

Nickel binding site 1 out of 1 in the Corynebacterium Glutamicum Oxyr, Oxidized Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Corynebacterium Glutamicum Oxyr, Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni401 b:71.2 occ:1.00 NE2 J:HIS138 2.3 43.8 1.0 O J:HOH569 2.3 54.4 1.0 NE2 B:HIS138 2.4 42.5 1.0 O B:HOH648 2.6 56.0 1.0 CD2 J:HIS138 3.0 43.0 1.0 O J:HOH593 3.2 64.4 1.0 CD2 B:HIS138 3.2 41.5 1.0 CE1 J:HIS138 3.4 42.9 1.0 CE1 B:HIS138 3.5 42.1 1.0 O J:HOH545 4.2 58.4 1.0 CG J:HIS138 4.3 41.1 1.0 ND1 J:HIS138 4.4 41.9 1.0 CG B:HIS138 4.5 40.3 1.0 CE J:LYS137 4.5 59.1 1.0 ND1 B:HIS138 4.6 41.2 1.0 O B:HOH673 4.6 47.2 1.0 OE1 B:GLN135 4.7 38.6 0.3 NZ J:LYS137 5.0 63.3 1.0

B.Pedre, D.Young, D.Charlier, A.Mourenza, L.A.Rosado, L.Marcos-Pascual, K.Wahni, E.Martens, A.G De La Rubia, V.V.Belousov, L.M.Mateos, J.Messens. Structural Snapshots of Oxyr Reveal the Peroxidatic Mechanism of H2O2SENSING. Proc. Natl. Acad. Sci. V. 115 11623 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30463959
DOI: 10.1073/PNAS.1807954115