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Copper in PDB 9kwv: Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite

Enzymatic activity of Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite

All present enzymatic activity of Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite:
1.7.2.1;

Protein crystallography data

The structure of Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite, PDB code: 9kwv 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) 28.84 / 0.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.371, 115.371, 84.336, 90, 90, 120
R / Rfree (%) 10.7 / 11.7

Other elements in 9kwv:

The structure of Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite (pdb code 9kwv). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite, PDB code: 9kwv:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9kwv

Go back to Copper Binding Sites List in 9kwv
Copper binding site 1 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:9.8
occ:1.00
 ND1 A:HIS143 2.0 9.6 1.0
ND1 A:HIS95 2.1 9.8 1.0
SD A:MET148 2.2 13.7 1.0
CE1 A:HIS143 2.8 10.3 1.0
CE1 A:HIS95 2.9 10.3 1.0
HE1 A:HIS143 3.0 12.3 1.0
HB3 A:HIS143 3.0 11.1 1.0
HE1 A:HIS95 3.0 12.4 1.0
CG A:HIS143 3.1 9.2 1.0
CG A:HIS95 3.2 9.6 1.0
HE3 A:TRP63 3.2 11.9 1.0
HB3 A:HIS95 3.3 12.2 1.0
CE A:MET148 3.3 15.5 1.0
HB2 A:ALA135 3.3 14.7 1.0
HE1 A:MET148 3.4 18.6 1.0
HG3 A:MET148 3.4 15.6 1.0
HB1 A:ALA135 3.4 14.7 1.0
CG A:MET148 3.4 13.0 1.0
HE3 A:MET148 3.4 18.6 1.0
HB3 A:ALA135 3.5 14.7 1.0
CB A:HIS143 3.5 9.2 1.0
CB A:ALA135 3.6 12.2 1.0
HA A:HIS95 3.7 12.0 1.0
CB A:HIS95 3.7 10.2 1.0
HB2 A:MET148 3.9 12.3 1.0
HB3 A:TRP63 3.9 11.5 1.0
CE3 A:TRP63 4.0 9.9 1.0
HA A:HIS143 4.0 10.7 1.0
NE2 A:HIS143 4.0 10.0 1.0
CB A:MET148 4.0 10.2 1.0
HB3 A:MET148 4.1 12.3 1.0
NE2 A:HIS95 4.1 10.4 1.0
HE2 A:MET148 4.1 18.6 1.0
CD2 A:HIS143 4.1 9.9 1.0
HG2 A:MET148 4.2 15.6 1.0
CD2 A:HIS95 4.2 10.4 1.0
CA A:HIS95 4.2 10.0 1.0
HB2 A:HIS143 4.3 11.1 1.0
HZ3 A:TRP63 4.3 12.9 1.0
CA A:HIS143 4.4 8.9 1.0
H A:SER96 4.4 11.7 1.0
HB A:THR137 4.4 13.4 1.0
O A:PRO94 4.5 10.8 1.0
HB2 A:HIS95 4.5 12.2 1.0
CZ3 A:TRP63 4.6 10.8 1.0
CB A:TRP63 4.7 9.6 1.0
HE2 A:HIS143 4.8 12.0 1.0
HB2 A:TRP63 4.8 11.5 1.0
HE2 A:HIS95 4.8 12.5 1.0
CD2 A:TRP63 4.9 9.8 1.0
O A:HIS143 5.0 9.3 1.0

Copper binding site 2 out of 6 in 9kwv

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Copper binding site 2 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:9.5
occ:0.98
 O2 A:NO2404 1.9 13.0 0.2
O1 A:NO2404 1.9 9.2 0.3
NE2 A:HIS100 2.0 8.6 1.0
NE2 A:HIS134 2.0 9.1 1.0
N A:NO2404 2.2 13.8 0.2
CL A:CL410 2.2 26.5 0.2
O2 A:NO2404 2.2 9.0 0.3
N A:NO2404 2.3 14.2 0.2
N A:NO2404 2.5 9.4 0.3
O A:HOH515 2.7 16.4 0.3
CE1 A:HIS100 3.0 8.2 1.0
O1 A:NO2404 3.0 13.2 0.2
CD2 A:HIS134 3.0 8.7 1.0
CE1 A:HIS134 3.0 9.1 1.0
CD2 A:HIS100 3.1 8.5 1.0
O2 A:NO2404 3.1 14.7 0.2
HE1 A:HIS100 3.1 9.9 1.0
HD2 A:HIS134 3.2 10.4 1.0
HE1 A:HIS134 3.2 10.9 1.0
HD2 A:HIS100 3.3 10.2 1.0
O1 A:NO2404 3.3 15.1 0.2
HD21 A:ASN98 3.4 13.9 1.0
ND2 A:ASN98 3.9 11.6 1.0
ND1 A:HIS100 4.1 8.3 1.0
ND1 A:HIS134 4.1 9.1 1.0
CG A:HIS134 4.1 8.4 1.0
CG A:HIS100 4.2 8.0 1.0
HD22 A:ASN98 4.4 13.9 1.0
CG A:ASN98 4.5 9.9 1.0
OD1 A:ASN98 4.6 10.4 1.0
O A:HOH693 4.8 11.8 1.0
HG2 A:MET132 4.8 10.4 1.0
HB3 A:SER274 4.9 9.8 1.0
HD1 A:HIS100 4.9 9.9 1.0
HD1 A:HIS134 4.9 11.0 1.0
HE2 A:MET132 4.9 10.7 1.0
HD12 A:ILE144 4.9 12.2 1.0

Copper binding site 3 out of 6 in 9kwv

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Copper binding site 3 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:10.9
occ:0.88
 ND1 A:HIS83 2.0 11.1 1.0
NE2 A:HIS42 2.0 11.4 1.0
O A:HOH667 2.1 21.3 1.0
O A:HOH778 2.3 16.5 1.0
H2 A:HOH778 2.4 19.8 1.0
CE1 A:HIS83 2.8 11.7 1.0
HE1 A:HIS83 3.0 14.0 1.0
CE1 A:HIS42 3.0 11.8 1.0
CD2 A:HIS42 3.0 10.8 1.0
CG A:HIS83 3.1 10.5 1.0
H1 A:HOH778 3.2 19.8 1.0
HE1 A:HIS42 3.2 14.2 1.0
HD2 A:HIS42 3.2 13.0 1.0
HB3 A:HIS83 3.3 12.7 1.0
HB2 A:HIS83 3.5 12.7 1.0
CB A:HIS83 3.6 10.6 1.0
HG22 A:VAL36 3.7 13.8 1.0
NE2 A:HIS83 4.0 12.1 1.0
ND1 A:HIS42 4.1 11.4 1.0
O A:HOH694 4.1 25.6 1.0
CG A:HIS42 4.2 10.3 1.0
CD2 A:HIS83 4.2 12.7 1.0
O A:HOH793 4.3 14.7 1.0
O A:HOH831 4.5 37.1 1.0
CG2 A:VAL36 4.6 11.5 1.0
HG12 A:VAL36 4.7 15.1 1.0
HE2 A:HIS83 4.8 14.5 1.0
HD1 A:HIS42 4.9 13.7 1.0
HG21 A:VAL36 4.9 13.8 1.0

Copper binding site 4 out of 6 in 9kwv

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Copper binding site 4 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:32.5
occ:0.53
 O A:HOH767 1.9 58.1 1.0
NE2 A:HIS39 2.0 17.2 1.0
CD2 A:HIS39 3.0 16.3 1.0
O A:HOH786 3.0 50.0 1.0
CE1 A:HIS39 3.0 16.9 1.0
HD2 A:HIS39 3.1 19.6 1.0
HE1 A:HIS39 3.2 20.2 1.0
HB2 A:PRO38 3.9 16.0 0.7
HB2 A:PRO38 4.1 14.8 0.3
ND1 A:HIS39 4.1 15.2 1.0
CG A:HIS39 4.1 14.2 1.0
HB3 A:PRO38 4.5 14.8 0.3
CB A:PRO38 4.8 12.3 0.3
CB A:PRO38 4.8 13.3 0.7
HG2 A:PRO38 4.8 15.2 0.7
HD1 A:HIS39 4.9 18.2 1.0

Copper binding site 5 out of 6 in 9kwv

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Copper binding site 5 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:12.9
occ:0.12
 N A:VAL249 2.0 8.8 1.0
O A:VAL249 2.0 10.1 1.0
O A:HOH541 2.1 10.3 1.0
OG1 A:THR248 2.1 9.9 1.0
H1 A:HOH541 2.6 12.3 1.0
C A:VAL249 2.7 9.1 1.0
CA A:VAL249 2.8 9.0 1.0
HB A:VAL249 2.9 11.8 1.0
C A:THR248 3.0 8.5 1.0
HA A:THR248 3.1 11.1 1.0
CB A:THR248 3.2 9.8 1.0
CA A:THR248 3.3 9.2 1.0
CB A:VAL249 3.3 9.8 1.0
HB2 A:PHE281 3.4 11.9 1.0
H A:THR282 3.4 12.3 1.0
HG23 A:THR248 3.6 13.0 1.0
HA A:VAL249 3.6 10.8 1.0
HG23 A:VAL249 3.6 13.3 1.0
HB A:THR248 3.9 11.8 1.0
CG2 A:THR248 4.0 10.8 1.0
N A:PHE250 4.0 8.6 1.0
CG2 A:VAL249 4.0 11.1 1.0
O A:THR282 4.1 10.9 1.0
HA A:PHE281 4.2 11.8 1.0
O A:THR248 4.2 9.2 1.0
CB A:PHE281 4.2 9.9 1.0
N A:THR282 4.3 10.3 1.0
HB3 A:PHE281 4.3 11.9 1.0
OD1 A:ASP251 4.4 13.1 1.0
HA A:PHE250 4.4 10.6 1.0
HG21 A:THR248 4.5 13.0 1.0
HB A:THR282 4.6 14.7 1.0
HG11 A:VAL249 4.6 12.4 1.0
CG1 A:VAL249 4.6 10.4 1.0
H A:ASP251 4.6 10.9 1.0
HG21 A:VAL249 4.6 13.3 1.0
CA A:PHE281 4.7 9.8 1.0
H A:PHE250 4.7 10.3 1.0
HG22 A:VAL249 4.7 13.3 1.0
CA A:PHE250 4.7 8.8 1.0
HG22 A:THR248 4.7 13.0 1.0
N A:THR248 4.7 9.0 1.0
N A:ASP251 4.9 9.1 1.0
CG A:ASP251 4.9 12.4 1.0
C A:PHE250 5.0 9.0 1.0
C A:PHE281 5.0 9.9 1.0

Copper binding site 6 out of 6 in 9kwv

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Copper binding site 6 out of 6 in the Structure of A D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite


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 D98N/C135A/G136A Mutant Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:45.0
occ:0.32
 O A:HOH512 1.9 34.4 1.0
OD2 A:ASP167 2.2 14.4 1.0
O A:HOH681 2.5 29.7 1.0
O A:HOH776 2.6 25.0 0.4
CG A:ASP167 3.0 14.5 1.0
OD1 A:ASP167 3.0 16.7 1.0
H A:LYS227 3.5 13.7 1.0
HA A:GLU226 3.7 14.5 1.0
O A:GLY225 4.1 14.2 1.0
O A:GLU165 4.1 15.0 1.0
N A:LYS227 4.3 11.4 1.0
O A:HOH721 4.3 40.3 0.8
HB3 A:LYS227 4.3 16.5 1.0
CB A:ASP167 4.4 13.2 1.0
CA A:GLU226 4.6 12.1 1.0
HB2 A:LYS227 4.6 16.5 1.0
HB2 A:ASP167 4.6 15.8 1.0
HG2 A:GLU226 4.8 15.4 1.0
HB3 A:ASP167 4.8 15.8 1.0
C A:GLU226 4.9 11.4 1.0
CB A:LYS227 4.9 13.8 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 10:06:26 2025

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