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

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

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

Protein crystallography data

The structure of D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite, PDB code: 9kwu 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) 32.22 / 1.12
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.334, 115.334, 84.332, 90, 90, 120
R / Rfree (%) 10.3 / 11.7

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 9kwu

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Copper binding site 1 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:9.4
occ:0.50
 SD A:MET148 2.0 12.2 0.7
ND1 A:HIS95 2.0 11.9 1.0
ND1 A:HIS143 2.1 11.7 1.0
SD A:MET148 2.2 9.6 0.3
CE1 A:HIS95 2.8 12.1 1.0
HB3 A:HIS143 2.9 12.5 1.0
HE1 A:HIS95 2.9 14.5 0.6
CE1 A:HIS143 3.1 12.2 1.0
CG A:HIS95 3.1 11.4 1.0
CG A:HIS143 3.1 10.5 1.0
HE3 A:MET148 3.1 14.9 0.7
HG3 A:MET148 3.1 12.2 0.3
HE3 A:TRP63 3.2 12.2 1.0
HB3 A:HIS95 3.2 14.1 1.0
CE A:MET148 3.2 9.2 0.3
HE1 A:HIS143 3.2 14.7 0.6
CE A:MET148 3.2 12.4 0.7
HB2 A:ALA135 3.3 13.2 1.0
HB1 A:ALA135 3.3 13.2 1.0
CG A:MET148 3.3 10.2 0.3
HB3 A:ALA135 3.4 13.2 1.0
CB A:HIS143 3.5 10.4 1.0
CB A:ALA135 3.5 11.0 1.0
CG A:MET148 3.5 11.8 0.7
CB A:HIS95 3.6 11.7 1.0
HG3 A:MET148 3.7 14.2 0.7
HA A:HIS95 3.8 13.8 1.0
HE1 A:MET148 3.8 14.9 0.7
HE2 A:MET148 3.8 14.9 0.7
HB2 A:MET148 3.9 11.6 0.7
NE2 A:HIS95 3.9 12.0 1.0
HB2 A:MET148 3.9 11.0 0.3
CE3 A:TRP63 3.9 10.1 1.0
HA A:HIS143 3.9 11.9 1.0
HB3 A:TRP63 4.0 11.3 1.0
CD2 A:HIS95 4.1 11.7 1.0
CB A:MET148 4.1 9.2 0.3
HG2 A:MET148 4.1 12.2 0.3
CB A:MET148 4.1 9.7 0.7
HB3 A:MET148 4.1 11.6 0.7
HB3 A:MET148 4.1 11.0 0.3
NE2 A:HIS143 4.2 11.8 1.0
HG2 A:MET148 4.2 14.2 0.7
CD2 A:HIS143 4.2 10.9 1.0
HB2 A:HIS143 4.2 12.5 1.0
HZ3 A:TRP63 4.2 13.5 0.8
CA A:HIS95 4.3 11.5 1.0
CA A:HIS143 4.3 10.0 1.0
HB2 A:HIS95 4.4 14.1 0.8
HB A:THR137 4.5 14.0 1.0
CZ3 A:TRP63 4.5 11.3 1.0
O A:PRO94 4.6 12.0 1.0
HE2 A:HIS95 4.6 14.4 1.0
CB A:TRP63 4.8 9.4 1.0
HG12 A:VAL93 4.8 16.8 0.9
HB2 A:TRP63 4.8 11.3 0.9
CD2 A:TRP63 4.9 10.2 1.0
O A:HIS143 4.9 10.1 1.0
HD2 A:HIS95 4.9 14.1 0.9
HE2 A:HIS143 5.0 14.2 0.9
C A:HIS143 5.0 9.5 1.0

Copper binding site 2 out of 6 in 9kwu

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Copper binding site 2 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:8.2
occ:0.52
 CU A:CU402 0.0 8.2 0.5
CU A:CU402 0.2 12.1 0.5
O2 A:NO2404 1.8 15.9 0.6
N A:NO2404 2.0 10.2 0.4
NE2 A:HIS134 2.0 9.0 1.0
O1 A:NO2405 2.1 10.9 0.5
NE2 A:HIS100 2.1 8.7 1.0
N A:NO2404 2.6 16.4 0.6
O1 A:NO2404 2.6 17.7 0.6
CE1 A:HIS134 3.0 8.3 1.0
O1 A:NO2404 3.0 9.7 0.4
O2 A:NO2404 3.0 12.3 0.4
N A:NO2405 3.0 11.5 0.5
CD2 A:HIS134 3.0 8.5 1.0
CE1 A:HIS100 3.1 8.2 1.0
CD2 A:HIS100 3.1 8.4 1.0
HE1 A:HIS134 3.2 10.0 0.8
HE1 A:HIS100 3.2 9.9 1.0
HD2 A:HIS134 3.2 10.2 0.9
HD2 A:HIS100 3.3 10.1 1.0
HD22 A:ASN98 3.4 13.5 0.6
ND2 A:ASN98 3.7 11.3 0.6
HD21 A:ASN98 3.8 12.9 0.5
HD21 A:ASN98 4.0 13.5 0.6
ND1 A:HIS134 4.1 9.0 1.0
CG A:HIS134 4.2 8.7 1.0
ND1 A:HIS100 4.2 8.5 1.0
CG A:ASN98 4.2 10.0 0.6
CG A:HIS100 4.2 8.1 1.0
O2 A:NO2405 4.3 12.7 0.5
OD1 A:ASN98 4.3 11.1 0.6
HB3 A:ASN98 4.6 10.7 0.5
O A:HOH680 4.6 9.2 0.4
ND2 A:ASN98 4.6 10.7 0.5
HB2 A:ASN98 4.6 10.7 0.5
O A:HOH744 4.8 25.3 0.5
HD1 A:HIS134 4.9 10.8 1.0
HB3 A:ASN98 4.9 11.4 0.6
HD1 A:HIS100 5.0 10.2 1.0
HE2 A:MET132 5.0 10.8 0.8

Copper binding site 3 out of 6 in 9kwu

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Copper binding site 3 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:12.1
occ:0.48
 CU A:CU402 0.0 12.1 0.5
CU A:CU402 0.2 8.2 0.5
O2 A:NO2404 1.8 15.9 0.6
NE2 A:HIS100 2.0 8.7 1.0
N A:NO2404 2.1 10.2 0.4
NE2 A:HIS134 2.1 9.0 1.0
O1 A:NO2405 2.2 10.9 0.5
N A:NO2404 2.6 16.4 0.6
O1 A:NO2404 2.7 17.7 0.6
CE1 A:HIS100 2.9 8.2 1.0
O2 A:NO2404 3.0 12.3 0.4
CD2 A:HIS100 3.0 8.4 1.0
N A:NO2405 3.0 11.5 0.5
HE1 A:HIS100 3.1 9.9 1.0
CD2 A:HIS134 3.1 8.5 1.0
O1 A:NO2404 3.1 9.7 0.4
CE1 A:HIS134 3.1 8.3 1.0
HD2 A:HIS134 3.3 10.2 0.9
HD2 A:HIS100 3.3 10.1 1.0
HE1 A:HIS134 3.3 10.0 0.8
HD22 A:ASN98 3.5 13.5 0.6
ND2 A:ASN98 3.8 11.3 0.6
HD21 A:ASN98 3.9 12.9 0.5
ND1 A:HIS100 4.0 8.5 1.0
CG A:HIS100 4.1 8.1 1.0
HD21 A:ASN98 4.2 13.5 0.6
ND1 A:HIS134 4.2 9.0 1.0
CG A:HIS134 4.3 8.7 1.0
O2 A:NO2405 4.3 12.7 0.5
CG A:ASN98 4.3 10.0 0.6
OD1 A:ASN98 4.4 11.1 0.6
O A:HOH680 4.6 9.2 0.4
HB3 A:ASN98 4.7 10.7 0.5
HB2 A:ASN98 4.8 10.7 0.5
ND2 A:ASN98 4.8 10.7 0.5
HD1 A:HIS100 4.8 10.2 1.0
HB3 A:SER274 4.9 9.8 1.0
O A:HOH744 5.0 25.3 0.5
HE2 A:MET132 5.0 10.8 0.8

Copper binding site 4 out of 6 in 9kwu

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Copper binding site 4 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:29.7
occ:0.61
 O A:HOH560 1.9 55.0 1.0
O A:HOH814 2.0 54.5 1.0
NE2 A:HIS39 2.0 17.3 1.0
O A:HOH769 2.3 61.3 1.0
O A:HOH747 2.4 53.4 1.0
CD2 A:HIS39 2.9 16.4 1.0
CE1 A:HIS39 3.0 17.1 1.0
HD2 A:HIS39 3.1 19.6 0.9
HB2 A:PRO38 4.0 15.7 0.7
CG A:HIS39 4.1 14.6 1.0
ND1 A:HIS39 4.1 15.7 1.0
HB2 A:PRO38 4.1 15.3 0.3
HB3 A:PRO38 4.5 15.3 0.3
O A:HOH665 4.8 40.5 0.6
CB A:PRO38 4.8 12.8 0.3
HG2 A:PRO38 4.8 15.8 0.7
CB A:PRO38 4.8 13.1 0.7
HD1 A:HIS39 4.9 18.9 0.3

Copper binding site 5 out of 6 in 9kwu

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Copper binding site 5 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:10.3
occ:0.89
 NE2 A:HIS42 2.0 11.6 1.0
ND1 A:HIS83 2.0 11.3 1.0
O A:HOH759 2.3 13.2 1.0
H1 A:HOH759 2.6 15.8 1.0
CE1 A:HIS83 2.9 11.2 1.0
H2 A:HOH759 2.9 15.8 1.0
HE1 A:HIS83 2.9 13.5 0.9
CE1 A:HIS42 3.0 11.6 1.0
CD2 A:HIS42 3.0 10.7 1.0
HE1 A:HIS42 3.1 13.9 0.9
CG A:HIS83 3.1 11.3 1.0
HD2 A:HIS42 3.2 12.8 0.7
HB3 A:HIS83 3.4 13.3 0.9
HB2 A:HIS83 3.5 13.3 1.0
CB A:HIS83 3.6 11.1 1.0
HG21 A:VAL36 3.7 14.0 0.9
NE2 A:HIS83 4.0 12.1 1.0
ND1 A:HIS42 4.1 11.2 1.0
O A:HOH700 4.1 13.9 0.6
CG A:HIS42 4.1 10.8 1.0
CD2 A:HIS83 4.2 12.7 1.0
O A:HOH799 4.4 14.4 1.0
H1 A:HOH799 4.5 17.3 1.0
O A:HOH849 4.6 33.0 1.0
CG2 A:VAL36 4.6 11.7 1.0
HG23 A:THR122 4.7 16.2 0.3
HG13 A:VAL36 4.7 15.5 1.0
HE2 A:HIS83 4.8 14.5 1.0
HD1 A:HIS42 4.9 13.5 1.0
HG22 A:VAL36 5.0 14.0 1.0

Copper binding site 6 out of 6 in 9kwu

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Copper binding site 6 out of 6 in the D98N/C135A Mutant of A 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 D98N/C135A Mutant of A Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:15.3
occ:0.22
 O A:HOH521 1.8 31.6 1.0
OD2 A:ASP167 2.1 14.8 1.0
O A:HOH833 2.2 37.5 0.7
O A:HOH507 2.3 40.2 0.7
O A:HOH762 2.3 42.6 1.0
O A:HOH671 2.4 26.3 1.0
CG A:ASP167 2.9 14.8 1.0
OD1 A:ASP167 2.9 17.3 1.0
H A:LYS227 3.4 13.8 1.0
HA A:GLU226 3.6 14.6 1.0
O A:GLY225 4.1 14.7 1.0
O A:GLU165 4.2 15.6 1.0
N A:LYS227 4.2 11.5 1.0
CB A:ASP167 4.3 13.2 1.0
HB3 A:LYS227 4.3 16.0 1.0
CA A:GLU226 4.5 12.2 1.0
HB2 A:ASP167 4.5 15.9 1.0
HB2 A:LYS227 4.5 16.0 0.6
HG2 A:GLU226 4.7 16.0 0.9
HB3 A:ASP167 4.8 15.9 0.8
C A:GLU226 4.8 11.7 1.0
CB A:LYS227 4.8 13.3 1.0
C A:GLY225 5.0 13.4 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 10:05:27 2025

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