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Copper in PDB 9kwt: Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans

Enzymatic activity of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans

All present enzymatic activity of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans:
1.7.2.1;

Protein crystallography data

The structure of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans, PDB code: 9kwt was solved by Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.11 / 0.96
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.126, 115.126, 84.43, 90, 90, 120
R / Rfree (%) 10 / 10.7

Other elements in 9kwt:

The structure of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans (pdb code 9kwt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans, PDB code: 9kwt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 9kwt

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Copper binding site 1 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:8.5
occ:1.00
 ND1 A:HIS95 2.0 8.5 1.0
ND1 A:HIS143 2.0 8.6 1.0
SG A:CYS135 2.2 8.4 1.0
SD A:MET148 2.6 8.4 1.0
HB3 A:HIS143 2.9 10.3 1.0
CE1 A:HIS143 2.9 8.9 1.0
CE1 A:HIS95 3.0 8.5 1.0
CG A:HIS95 3.0 8.3 1.0
CG A:HIS143 3.0 8.1 1.0
HA A:HIS95 3.1 10.4 1.0
HE1 A:HIS143 3.1 10.7 1.0
HB3 A:HIS95 3.1 10.5 1.0
HE1 A:HIS95 3.1 10.2 1.0
CB A:CYS135 3.2 8.1 1.0
HB2 A:CYS135 3.2 9.7 1.0
HE2 A:MET148 3.2 11.9 1.0
HB3 A:CYS135 3.3 9.7 1.0
CB A:HIS95 3.4 8.8 1.0
CE A:MET148 3.4 9.9 1.0
CB A:HIS143 3.5 8.6 1.0
HB A:THR137 3.6 11.2 1.0
HE3 A:MET148 3.7 11.9 1.0
CA A:HIS95 3.7 8.7 1.0
H A:SER96 3.8 10.0 1.0
HE3 A:TRP63 3.9 10.2 1.0
NE2 A:HIS143 4.0 9.2 1.0
O A:PRO94 4.0 9.3 0.7
O A:PRO94 4.0 9.3 0.3
CG A:MET148 4.1 8.4 1.0
NE2 A:HIS95 4.1 8.8 1.0
HB2 A:HIS143 4.1 10.3 1.0
CD2 A:HIS143 4.1 8.8 1.0
CD2 A:HIS95 4.1 8.7 1.0
HB2 A:MET148 4.3 9.2 1.0
HE1 A:MET148 4.3 11.9 1.0
OG1 A:THR137 4.3 9.5 1.0
HA A:HIS143 4.3 9.5 1.0
HG3 A:MET148 4.3 10.1 1.0
HB2 A:HIS95 4.3 10.5 1.0
CB A:THR137 4.4 9.4 1.0
H A:THR137 4.4 11.1 1.0
HB3 A:MET148 4.5 9.2 1.0
N A:SER96 4.5 8.3 1.0
CA A:HIS143 4.5 7.9 1.0
CB A:MET148 4.5 7.7 1.0
CE3 A:TRP63 4.6 8.5 1.0
HZ3 A:TRP63 4.6 11.5 1.0
CA A:CYS135 4.6 7.6 1.0
C A:HIS95 4.7 8.5 1.0
N A:HIS95 4.7 9.0 1.0
HE2 A:HIS143 4.8 11.1 1.0
HG2 A:MET148 4.8 10.1 1.0
C A:PRO94 4.8 8.9 0.7
C A:PRO94 4.8 9.3 0.3
HB3 A:TRP63 4.8 10.0 1.0
HG23 A:THR137 4.8 13.0 1.0
HA A:CYS135 4.9 9.1 1.0
HE2 A:HIS95 4.9 10.6 1.0
HG A:SER96 4.9 10.8 1.0
HD2 A:HIS143 5.0 10.6 1.0
CZ3 A:TRP63 5.0 9.6 1.0

Copper binding site 2 out of 7 in 9kwt

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Copper binding site 2 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:8.9
occ:0.95
 NE2 A:HIS100 2.0 7.8 1.0
O A:HOH504 2.0 21.1 0.2
NE2 A:HIS134 2.0 8.0 1.0
CL A:CL403 2.1 11.7 0.7
O A:HOH504 2.4 9.5 0.3
CE1 A:HIS100 2.9 7.0 1.0
CD2 A:HIS134 3.0 7.4 1.0
CE1 A:HIS134 3.0 7.9 1.0
CD2 A:HIS100 3.0 7.3 1.0
HE1 A:HIS100 3.1 8.4 1.0
HD2 A:HIS134 3.1 8.9 1.0
HE1 A:HIS134 3.2 9.5 1.0
HD2 A:HIS100 3.3 8.7 1.0
HD22 A:ASN98 3.4 13.7 1.0
O A:HOH830 3.5 19.5 0.3
O A:HOH783 3.7 13.8 0.3
ND2 A:ASN98 3.9 11.4 1.0
ND1 A:HIS100 4.1 6.9 1.0
ND1 A:HIS134 4.1 7.8 1.0
CG A:HIS134 4.1 7.3 1.0
CG A:HIS100 4.2 6.9 1.0
HD21 A:ASN98 4.3 13.7 1.0
CG A:ASN98 4.4 9.2 1.0
OD1 A:ASN98 4.5 9.6 1.0
O A:HOH685 4.7 12.5 0.7
O A:HOH694 4.8 12.6 1.0
HD11 A:ILE144 4.8 11.4 1.0
HG2 A:MET132 4.8 8.2 1.0
HE2 A:MET132 4.8 8.9 1.0
HD1 A:HIS100 4.8 8.3 1.0
HB3 A:SER274 4.8 8.5 1.0
HD1 A:HIS134 4.9 9.4 1.0

Copper binding site 3 out of 7 in 9kwt

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Copper binding site 3 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:32.7
occ:0.66
 NE2 A:HIS39 2.0 15.2 1.0
O A:HOH782 2.5 54.1 1.0
O A:HOH821 2.8 41.2 1.0
CE1 A:HIS39 2.9 15.2 1.0
CD2 A:HIS39 3.0 14.1 1.0
HE1 A:HIS39 3.1 18.3 1.0
HD2 A:HIS39 3.2 16.9 1.0
HB2 A:PRO38 4.0 14.8 0.7
ND1 A:HIS39 4.0 13.6 1.0
CG A:HIS39 4.1 12.5 1.0
HB2 A:PRO38 4.2 14.1 0.3
O A:HOH917 4.5 46.2 1.0
HB3 A:PRO38 4.6 14.1 0.3
HD1 A:HIS39 4.8 16.3 1.0
CB A:PRO38 4.8 11.7 0.3
CB A:PRO38 4.9 12.4 0.7
HG2 A:PRO38 5.0 14.8 0.7

Copper binding site 4 out of 7 in 9kwt

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Copper binding site 4 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:8.5
occ:0.86
 OE2 A:GLU53 2.0 9.9 1.0
O A:HOH574 2.1 13.7 1.0
H1 A:HOH574 2.4 16.4 1.0
CD A:GLU53 2.6 9.1 1.0
OE1 A:GLU53 2.6 10.4 1.0
H2 A:HOH574 2.8 16.4 1.0
H A:GLY57 3.1 12.7 0.3
H A:GLY57 3.2 12.7 0.7
N A:GLY57 4.0 10.6 1.0
HA2 A:GLY57 4.0 14.2 1.0
HA A:LYS56 4.1 12.5 0.7
CG A:GLU53 4.1 9.1 1.0
O A:HOH731 4.1 15.9 1.0
HA A:LYS56 4.2 14.7 0.3
HG3 A:GLU53 4.3 10.9 1.0
CA A:GLY57 4.5 11.8 1.0
HG2 A:GLU53 4.5 10.9 1.0
HB2 A:GLU53 4.8 10.0 1.0
HB3 A:LYS56 4.8 14.4 0.7
CA A:LYS56 4.9 10.4 0.7
HG3 A:LYS56 4.9 21.4 0.3
C A:LYS56 4.9 10.0 0.7
C A:LYS56 5.0 10.7 0.3

Copper binding site 5 out of 7 in 9kwt

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Copper binding site 5 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:15.8
occ:0.43
 O A:HOH525 2.0 31.9 1.0
OD2 A:ASP167 2.1 16.4 1.0
O A:HOH854 2.2 38.4 1.0
O A:HOH638 2.3 24.7 1.0
O A:HOH781 2.5 39.7 1.0
O A:HOH503 2.7 42.3 1.0
CG A:ASP167 2.9 13.6 1.0
OD1 A:ASP167 3.0 13.1 1.0
H A:LYS227 3.4 12.4 0.8
H A:LYS227 3.4 12.8 0.2
HA A:GLU226 3.6 13.0 1.0
HB3 A:LYS227 3.9 14.6 0.2
O A:GLU165 4.1 14.0 1.0
O A:GLY225 4.2 12.7 1.0
N A:LYS227 4.2 10.7 0.2
N A:LYS227 4.2 10.3 0.8
CB A:ASP167 4.3 12.7 1.0
HB3 A:LYS227 4.3 15.0 0.8
HB2 A:ASP167 4.5 15.2 1.0
CA A:GLU226 4.5 10.8 1.0
HB2 A:LYS227 4.5 15.0 0.8
O A:HOH751 4.6 45.6 1.0
HB2 A:LYS227 4.6 14.6 0.2
CB A:LYS227 4.7 12.1 0.2
HB3 A:ASP167 4.7 15.2 1.0
HG2 A:GLU226 4.7 14.4 1.0
C A:GLU226 4.8 10.2 1.0
CB A:LYS227 4.8 12.5 0.8

Copper binding site 6 out of 7 in 9kwt

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Copper binding site 6 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:8.3
occ:0.15
 O A:HOH540 1.7 35.9 1.0
O A:HOH538 1.8 14.8 1.0
O A:HOH851 2.1 49.0 1.0
OE2 A:GLU239 2.2 12.1 0.7
O A:HOH551 2.4 26.4 1.0
OE2 A:GLU239 2.7 13.0 0.3
CD A:GLU239 2.9 9.4 0.7
OE1 A:GLU239 3.0 9.6 0.7
OE1 A:GLU239 3.0 12.0 0.3
CD A:GLU239 3.1 11.6 0.3
HE2 A:HIS298 3.3 9.2 1.0
HD2 A:PRO191 3.4 10.3 1.0
HD3 A:PRO191 3.5 10.3 1.0
HG12 A:VAL190 3.6 13.1 1.0
O A:HOH505 3.6 24.2 1.0
O A:HOH824 3.7 30.1 1.0
HA A:VAL190 3.8 9.8 1.0
O A:HOH771 3.8 22.9 1.0
CD A:PRO191 3.8 8.5 1.0
NE2 A:HIS298 4.1 7.7 1.0
O A:HOH565 4.2 13.4 1.0
CG A:GLU239 4.3 8.5 0.7
HG3 A:GLU239 4.4 12.8 0.3
CG A:GLU239 4.4 10.7 0.3
HB A:VAL190 4.4 11.2 1.0
HG3 A:PRO191 4.5 11.3 1.0
CG1 A:VAL190 4.5 10.9 1.0
HE1 A:HIS298 4.5 9.6 1.0
HG3 A:GLU239 4.5 10.2 0.7
O A:HOH867 4.6 20.4 0.3
HG2 A:GLU239 4.7 10.2 0.7
CA A:VAL190 4.7 8.2 1.0
CG A:PRO191 4.7 9.4 1.0
CE1 A:HIS298 4.7 8.0 1.0
CB A:VAL190 4.8 9.4 1.0
HG11 A:VAL190 4.8 13.1 1.0
HG2 A:GLU239 4.9 12.8 0.3

Copper binding site 7 out of 7 in 9kwt

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Copper binding site 7 out of 7 in the Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of A Copper-Containing Nitrite Reductase (D98N/G136A Mutant) From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:24.5
occ:0.10
 N A:VAL249 2.0 7.9 1.0
O A:VAL249 2.1 9.1 1.0
OG1 A:THR248 2.1 8.4 1.0
C A:VAL249 2.7 7.8 1.0
CA A:VAL249 2.8 8.0 1.0
HB A:VAL249 2.8 10.3 1.0
C A:THR248 3.0 7.4 1.0
HA A:THR248 3.1 9.5 1.0
CB A:THR248 3.2 8.3 1.0
CA A:THR248 3.3 7.9 1.0
CB A:VAL249 3.3 8.6 1.0
H A:THR282 3.4 10.8 1.0
HB2 A:PHE281 3.5 10.2 1.0
HG22 A:VAL249 3.6 12.2 1.0
HA A:VAL249 3.6 9.6 1.0
HG23 A:THR248 3.7 11.7 1.0
HB A:THR248 3.9 10.0 1.0
CG2 A:THR248 4.0 9.7 1.0
CG2 A:VAL249 4.0 10.1 1.0
N A:PHE250 4.0 7.5 1.0
O A:THR282 4.1 9.7 1.0
O A:THR248 4.2 8.0 1.0
HA A:PHE281 4.2 10.5 1.0
N A:THR282 4.2 9.0 1.0
CB A:PHE281 4.2 8.5 1.0
HB3 A:PHE281 4.3 10.2 1.0
OD1 A:ASP251 4.4 10.6 1.0
HG21 A:THR248 4.5 11.7 1.0
HA A:PHE250 4.5 9.3 1.0
HB A:THR282 4.5 13.5 1.0
HG12 A:VAL249 4.6 11.7 1.0
CG1 A:VAL249 4.6 9.8 1.0
HG23 A:VAL249 4.6 12.2 1.0
H A:ASP251 4.6 9.5 1.0
HG21 A:VAL249 4.7 12.2 1.0
CA A:PHE281 4.7 8.7 1.0
H A:PHE250 4.7 9.0 1.0
N A:THR248 4.7 7.9 1.0
HG22 A:THR248 4.7 11.7 1.0
CA A:PHE250 4.7 7.7 1.0
N A:ASP251 4.9 7.9 1.0
CG A:ASP251 4.9 10.3 1.0
C A:PHE250 5.0 7.8 1.0

Reference:

Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada. Structural Basis of Cuproenzyme Nitrite Reduction at the Level of A Single Hydrogen Atom. J.Biol.Chem. 10290 2025.
ISSN: ESSN 1083-351X
PubMed: 40436316
DOI: 10.1016/J.JBC.2025.110290
Page generated: Mon Jul 14 10:04:24 2025

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