Chlorine in PDB 4zk8: Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)

The structure of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined), PDB code: 4zk8 was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.06 / 1.15
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.054, 115.054, 84.417, 90.00, 90.00, 120.00
R / Rfree (%)	12 / 14.6

The structure of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) also contains other interesting chemical elements:

Copper

(Cu)

25 atoms

The binding sites of Chlorine atom in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) (pdb code 4zk8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined), PDB code: 4zk8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl419 b:13.0 occ:0.70 O A:HOH507 2.0 18.3 0.5 CU A:CU402 2.2 9.2 0.9 O A:HOH802 3.0 19.3 1.0 NE2 A:HIS134 3.3 9.0 1.0 CE1 A:HIS134 3.4 8.7 1.0 OD2 A:ASP98 3.9 12.9 1.0 NE2 A:HIS100 4.0 8.2 1.0 O A:HOH512 4.4 20.6 1.0 CD2 A:HIS134 4.6 8.8 1.0 ND1 A:HIS134 4.8 8.5 1.0 CE1 A:HIS100 4.8 8.2 1.0 CD2 A:HIS100 4.9 8.7 1.0 CG A:ASP98 4.9 10.9 1.0

Chlorine binding site 2 out of 3 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl420 b:50.4 occ:0.50 CL A:CL420 0.0 50.4 0.5 CL A:CL420 1.1 53.0 0.5 O A:HOH860 3.6 27.3 0.3 O A:HOH583 3.8 21.0 0.6 O A:HOH746 3.8 20.5 0.5 OD1 A:ASN158 3.9 27.1 0.5 NZ A:LYS157 4.4 50.9 0.5 OD1 A:ASN158 4.7 52.2 0.5 CE A:LYS157 4.8 38.2 0.5 O A:HOH736 4.8 28.2 1.0 CD A:LYS157 4.8 29.3 0.5 CU A:CU416 4.8 17.2 0.6 CG A:ASN158 4.8 24.0 0.5 ND2 A:ASN158 4.8 29.8 0.5 CD A:LYS157 4.9 30.3 0.5

Chlorine binding site 3 out of 3 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl420 b:53.0 occ:0.50 CL A:CL420 0.0 53.0 0.5 CL A:CL420 1.1 50.4 0.5 NZ A:LYS157 3.3 50.9 0.5 O A:HOH583 3.4 21.0 0.6 O A:HOH860 3.4 27.3 0.3 CE A:LYS157 3.8 38.2 0.5 CD A:LYS157 3.8 29.3 0.5 CD A:LYS157 3.9 30.3 0.5 OD1 A:ASN158 4.0 27.1 0.5 NZ A:LYS157 4.2 50.0 0.5 O A:HOH746 4.2 20.5 0.5 CE A:LYS157 4.3 37.9 0.5 CU A:CU416 4.8 17.2 0.6 O A:HOH736 4.8 28.2 1.0 ND2 A:ASN158 4.9 29.8 0.5 CG A:LYS157 4.9 25.6 0.5 CG A:ASN158 4.9 24.0 0.5 CG A:LYS157 4.9 25.1 0.5

Y.Fukuda, K.M.Tse, M.Lintuluoto, Y.Fukunishi, E.Mizohata, H.Matsumura, H.Takami, M.Nojiri, T.Inoue. Structural Insights Into the Function of A Thermostable Copper-Containing Nitrite Reductase J.Biochem. V. 155 123 2014.
ISSN: ISSN 0021-924X
PubMed: 24293549
DOI: 10.1093/JB/MVT107