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

Protein crystallography data

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

Other elements in 4zk8:

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

Copper (Cu) 25 atoms

Chlorine Binding Sites:

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 4zk8

Go back to Chlorine Binding Sites List in 4zk8
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 4zk8

Go back to Chlorine Binding Sites List in 4zk8
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 4zk8

Go back to Chlorine Binding Sites List in 4zk8
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

Reference:

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
Page generated: Sat Dec 12 11:28:29 2020

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