Nickel in PDB 6bwr: LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel

The structure of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel, PDB code: 6bwr was solved by M.Fellner, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.32 / 1.81
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	96.634, 96.634, 96.634, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 19.2

The binding sites of Nickel atom in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel (pdb code 6bwr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel, PDB code: 6bwr:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:25.6 occ:0.33 OD2 A:ASP370 1.9 54.0 1.0 O A:HOH610 1.9 26.1 1.0 CG A:ASP370 3.1 43.8 1.0 OD1 A:ASP370 3.7 43.3 1.0 O A:HOH663 4.0 36.0 1.0 CB A:ASP370 4.2 41.2 1.0

Nickel binding site 2 out of 4 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:43.3 occ:1.00 OE2 A:GLU289 2.0 45.7 1.0 CD A:GLU289 3.2 33.2 1.0 OE1 A:GLU289 3.9 36.0 1.0 O A:HOH636 4.0 36.4 1.0 CG A:GLU289 4.3 26.7 1.0

Nickel binding site 3 out of 4 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:25.5 occ:1.00 NE2 B:HIS399 2.1 35.5 1.0 O B:HOH624 2.1 24.2 1.0 O B:HOH636 2.2 29.2 1.0 CD2 B:HIS399 3.0 27.7 1.0 CE1 B:HIS399 3.1 25.9 1.0 O B:GLN397 4.1 22.5 1.0 ND1 B:HIS399 4.2 24.6 1.0 CG B:HIS399 4.2 26.7 1.0 O B:GLN396 4.3 20.7 1.0 C B:GLN397 4.8 19.0 1.0 CA B:GLN397 5.0 22.2 1.0

Nickel binding site 4 out of 4 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:42.7 occ:1.00 OD1 B:ASP330 2.1 43.7 1.0 O B:HOH649 2.2 42.5 1.0 O B:HOH654 2.2 37.5 1.0 O B:HOH659 2.2 44.9 1.0 CG B:ASP330 3.0 32.7 1.0 OD2 B:ASP330 3.2 38.2 1.0 O B:HOH622 3.7 23.5 1.0 CB B:ASP330 4.4 24.9 1.0 O B:HOH632 4.5 22.0 1.0 CB B:ASN327 4.8 23.2 1.0

B.Desguin, M.Fellner, O.Riant, J.Hu, R.P.Hausinger, P.Hols, P.Soumillion. Biosynthesis of the Nickel-Pincer Nucleotide Cofactor of Lactate Racemase Requires A Ctp-Dependent Cyclometallase. J. Biol. Chem. V. 293 12303 2018.
ISSN: ESSN 1083-351X
PubMed: 29887527
DOI: 10.1074/JBC.RA118.003741