Nickel in PDB 2r9z: Glutathione Amide Reductase From Chromatium Gracile

The structure of Glutathione Amide Reductase From Chromatium Gracile, PDB code: 2r9z was solved by F.Van Petegem, B.Vergauwen, S.Savvides, D.De Vos, J.Van Beeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	71.933, 71.933, 223.854, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.6

The structure of Glutathione Amide Reductase From Chromatium Gracile also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Nickel atom in the Glutathione Amide Reductase From Chromatium Gracile (pdb code 2r9z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Glutathione Amide Reductase From Chromatium Gracile, PDB code: 2r9z:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Glutathione Amide Reductase From Chromatium Gracile


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Glutathione Amide Reductase From Chromatium Gracile within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni466 b:36.7 occ:1.00 O A:HOH699 1.6 23.9 1.0 O A:HOH745 1.9 33.1 1.0 NE2 A:HIS120 2.2 28.0 1.0 O A:HOH744 2.3 45.6 1.0 CD2 A:HIS120 3.2 25.3 1.0 CE1 A:HIS120 3.2 28.5 1.0 O A:HOH746 3.4 48.5 1.0 OD2 A:ASP118 4.1 32.4 1.0 OG1 A:THR121 4.3 25.5 1.0 ND1 A:HIS120 4.3 29.3 1.0 CG A:HIS120 4.3 27.8 1.0 OD1 A:ASP118 4.6 30.2 1.0 CG A:ASP118 4.7 29.5 1.0

Nickel binding site 2 out of 4 in the Glutathione Amide Reductase From Chromatium Gracile


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Glutathione Amide Reductase From Chromatium Gracile within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni468 b:36.5 occ:1.00 N A:GLN3 1.8 31.9 1.0 ND1 A:HIS4 1.9 29.4 1.0 N A:THR2 2.0 32.9 1.0 N A:HIS4 2.0 30.6 1.0 C A:THR2 2.7 32.8 1.0 CE1 A:HIS4 2.8 30.6 1.0 C A:GLN3 2.8 31.3 1.0 CA A:GLN3 2.8 31.7 1.0 CA A:THR2 2.9 33.1 1.0 CG A:HIS4 2.9 30.9 1.0 CA A:HIS4 3.1 30.1 1.0 CB A:HIS4 3.3 30.8 1.0 N A:PHE5 3.7 28.7 1.0 C A:HIS4 3.8 29.6 1.0 O A:HOH666 3.8 44.7 1.0 CB A:GLN3 3.9 32.3 1.0 O A:THR2 3.9 32.2 1.0 NE2 A:HIS4 3.9 31.0 1.0 CD2 A:HIS4 4.0 30.6 1.0 CD2 A:PHE5 4.0 27.0 1.0 CB A:THR2 4.0 34.1 1.0 O A:GLN3 4.0 31.9 1.0 O A:HOH667 4.0 31.8 1.0 CG2 A:THR2 4.1 32.3 1.0 CE2 A:PHE5 4.2 26.2 1.0 CG A:PHE5 4.8 27.3 1.0 O A:SER130 4.8 24.9 1.0 O A:HIS4 4.8 30.2 1.0 CA A:PHE5 4.9 27.9 1.0 CZ A:PHE5 5.0 27.1 1.0

Nickel binding site 3 out of 4 in the Glutathione Amide Reductase From Chromatium Gracile


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Glutathione Amide Reductase From Chromatium Gracile within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni466 b:37.0 occ:1.00 O B:HOH696 1.8 27.8 1.0 O B:HOH698 1.8 34.6 1.0 NE2 B:HIS120 2.2 30.2 1.0 O B:HOH697 2.5 49.1 1.0 CD2 B:HIS120 3.2 25.6 1.0 CE1 B:HIS120 3.2 29.8 1.0 OD2 B:ASP118 4.2 31.9 1.0 CG2 B:THR121 4.3 26.8 1.0 ND1 B:HIS120 4.3 30.1 1.0 CG B:HIS120 4.3 28.2 1.0 OD1 B:ASP118 4.7 28.5 1.0 CG B:ASP118 4.8 29.3 1.0

Nickel binding site 4 out of 4 in the Glutathione Amide Reductase From Chromatium Gracile


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Glutathione Amide Reductase From Chromatium Gracile within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni468 b:36.6 occ:1.00 ND1 B:HIS4 1.8 28.3 1.0 N B:GLN3 1.9 33.3 1.0 N B:THR2 2.0 34.3 1.0 N B:HIS4 2.1 31.3 1.0 C B:THR2 2.8 34.0 1.0 CE1 B:HIS4 2.8 29.9 1.0 CG B:HIS4 2.9 30.2 1.0 C B:GLN3 2.9 32.0 1.0 CA B:GLN3 2.9 32.5 1.0 CA B:THR2 2.9 34.4 1.0 CA B:HIS4 3.1 30.6 1.0 CB B:HIS4 3.2 31.2 1.0 N B:PHE5 3.7 29.5 1.0 C B:HIS4 3.8 30.3 1.0 CB B:GLN3 3.9 33.1 1.0 NE2 B:HIS4 3.9 28.9 1.0 O B:THR2 3.9 33.7 1.0 CD2 B:HIS4 4.0 30.2 1.0 CB B:THR2 4.0 35.1 1.0 CG2 B:THR2 4.0 33.7 1.0 O B:GLN3 4.1 32.4 1.0 CD2 B:PHE5 4.1 29.9 1.0 CE2 B:PHE5 4.3 29.6 1.0 CG B:PHE5 4.8 29.8 1.0 O B:HIS4 4.8 31.0 1.0 O B:SER130 4.8 26.1 1.0 CA B:PHE5 5.0 28.9 1.0

F.Van Petegem, D.De Vos, S.Savvides, B.Vergauwen, J.Van Beeumen. Understanding Nicotinamide Dinucleotide Cofactor and Substrate Specificity in Class I Flavoprotein Disulfide Oxidoreductases: Crystallographic Analysis of A Glutathione Amide Reductase. J.Mol.Biol. V. 374 883 2007.
ISSN: ISSN 0022-2836
PubMed: 17977556
DOI: 10.1016/J.JMB.2007.09.072