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Copper in PDB 9kvm: Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate

Enzymatic activity of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate

All present enzymatic activity of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate:
1.7.2.1;

Protein crystallography data

The structure of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate, PDB code: 9kvm 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) N/A / 1.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 116.172, 116.172, 85.612, 90, 90, 120
R / Rfree (%) 14.6 / 18.3

Copper Binding Sites:

The binding sites of Copper atom in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate (pdb code 9kvm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate, PDB code: 9kvm:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 9kvm

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Copper binding site 1 out of 4 in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:22.7
occ:0.89
 ND1 A:HIS143 2.0 23.6 1.0
ND1 A:HIS95 2.1 24.2 1.0
SD A:MET148 2.2 28.5 1.0
CE1 A:HIS143 2.9 24.8 1.0
CE1 A:HIS95 2.9 25.4 1.0
HB3 A:HIS143 2.9 16.8 1.0
HE1 A:HIS143 3.0 33.7 1.0
HE1 A:HIS95 3.0 32.6 1.0
CG A:HIS143 3.1 22.6 1.0
CG A:HIS95 3.2 23.2 1.0
HB3 A:HIS95 3.2 24.8 1.0
HE3 A:TRP63 3.2 20.3 1.0
HB3 A:ALA135 3.3 25.5 1.0
CE A:MET148 3.3 33.2 1.0
HE3 A:MET148 3.3 42.8 1.0
HB2 A:ALA135 3.3 34.3 1.0
HG3 A:MET148 3.4 23.2 1.0
CG A:MET148 3.4 28.2 1.0
HE2 A:MET148 3.5 39.5 1.0
CB A:HIS143 3.5 21.8 1.0
HB1 A:ALA135 3.6 33.4 1.0
CB A:ALA135 3.6 26.9 1.0
CB A:HIS95 3.6 23.0 1.0
HA A:HIS95 3.7 28.1 1.0
HB2 A:MET148 3.9 26.9 1.0
HB3 A:TRP63 4.0 25.5 1.0
CE3 A:TRP63 4.0 23.8 1.0
HA A:HIS143 4.0 22.8 1.0
NE2 A:HIS143 4.0 25.2 1.0
NE2 A:HIS95 4.1 24.5 1.0
CB A:MET148 4.1 24.3 1.0
HE1 A:MET148 4.1 31.7 1.0
CD2 A:HIS143 4.2 23.2 1.0
HB3 A:MET148 4.2 33.9 1.0
HG2 A:MET148 4.2 40.9 1.0
CD2 A:HIS95 4.2 23.6 1.0
CA A:HIS95 4.2 24.0 1.0
HB2 A:HIS143 4.3 25.3 1.0
HZ3 A:TRP63 4.3 24.8 1.0
CA A:HIS143 4.3 21.3 1.0
HB A:THR137 4.4 21.1 1.0
H A:SER96 4.4 24.6 0.9
D A:SER96 4.4 22.9 0.1
O A:PRO94 4.5 24.7 1.0
HB2 A:HIS95 4.5 30.2 1.0
CZ3 A:TRP63 4.6 24.9 1.0
HB2 A:TRP63 4.8 18.6 1.0
CB A:TRP63 4.8 21.3 1.0
DE2 A:HIS143 4.8 28.3 1.0
DE2 A:HIS95 4.8 30.9 1.0
CD2 A:TRP63 4.9 23.2 1.0
O A:HIS143 5.0 22.8 1.0

Copper binding site 2 out of 4 in 9kvm

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Copper binding site 2 out of 4 in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:22.7
occ:1.00
 O A:HOH502 1.9 32.4 0.5
O A:HOH502 2.0 24.3 0.5
NE2 A:HIS100 2.0 21.2 1.0
NE2 A:HIS134 2.1 21.3 1.0
D1 A:HOH502 2.2 32.7 0.5
D2 A:HOH502 2.3 30.6 0.5
O A:HOH691 2.4 28.2 0.1
O1 A:FMT405 2.4 41.7 0.5
D1 A:HOH691 2.6 28.3 0.1
D1 A:HOH502 2.6 21.4 0.5
CE1 A:HIS100 3.0 20.2 1.0
CD2 A:HIS100 3.0 21.0 1.0
CE1 A:HIS134 3.0 20.8 1.0
D2 A:HOH691 3.1 27.9 0.1
CD2 A:HIS134 3.1 20.7 1.0
HE1 A:HIS100 3.2 16.8 1.0
HD2 A:HIS100 3.2 25.4 1.0
HE1 A:HIS134 3.2 19.1 1.0
HD2 A:HIS134 3.2 24.0 1.0
C A:FMT405 3.4 44.1 0.5
CU A:CU404 3.7 19.9 0.1
O2 A:FMT405 3.8 41.6 0.5
OD2 A:ASP98 3.8 25.5 1.0
ND1 A:HIS100 4.1 21.2 1.0
ND1 A:HIS134 4.2 21.5 1.0
CG A:HIS100 4.2 21.2 1.0
CG A:HIS134 4.2 21.3 1.0
O A:HOH708 4.3 28.6 0.2
D2 A:HOH708 4.4 27.1 0.2
D A:FMT405 4.4 49.6 0.5
CG A:ASP98 4.4 23.3 1.0
D2 A:HOH587 4.5 30.2 0.9
OD1 A:ASP98 4.5 24.0 1.0
D1 A:HOH501 4.6 35.5 0.4
O A:HOH587 4.7 26.8 0.9
D1 A:HOH501 4.8 35.4 0.6
HB3 A:SER274 4.9 21.1 1.0
DD1 A:HIS100 4.9 18.1 1.0
HD1 A:HIS134 4.9 22.1 0.3
DD1 A:HIS134 4.9 16.4 0.7
DG A:SER274 4.9 30.4 0.3
HE3 A:MET132 5.0 27.4 1.0
D2 A:HOH501 5.0 33.5 0.4

Copper binding site 3 out of 4 in 9kvm

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Copper binding site 3 out of 4 in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:23.3
occ:0.91
 O A:HOH595 2.0 36.1 1.0
NE2 A:HIS42 2.0 25.0 1.0
ND1 A:HIS83 2.0 23.9 1.0
O A:HOH689 2.3 30.6 1.0
D1 A:HOH595 2.4 35.6 1.0
D2 A:HOH595 2.5 37.0 1.0
D2 A:HOH689 2.8 32.5 1.0
CE1 A:HIS83 2.9 25.8 1.0
D1 A:HOH689 2.9 33.0 1.0
CE1 A:HIS42 2.9 26.6 1.0
HE1 A:HIS83 3.0 34.0 1.0
CD2 A:HIS42 3.0 24.6 1.0
HE1 A:HIS42 3.1 33.4 1.0
CG A:HIS83 3.1 25.3 1.0
HD2 A:HIS42 3.2 26.2 1.0
HB3 A:HIS83 3.3 21.3 1.0
HB2 A:HIS83 3.5 32.5 1.0
CB A:HIS83 3.6 23.4 1.0
D1 A:HOH713 3.9 36.3 1.0
NE2 A:HIS83 4.0 26.1 1.0
O A:HOH651 4.1 59.2 1.0
ND1 A:HIS42 4.1 25.4 1.0
CG A:HIS42 4.1 24.5 1.0
CD2 A:HIS83 4.2 25.9 1.0
HG23 A:VAL36 4.2 29.7 1.0
HG21 A:VAL36 4.2 30.1 1.0
O A:HOH700 4.4 39.4 1.0
D1 A:HOH651 4.4 65.1 1.0
O A:HOH715 4.4 44.4 1.0
D1 A:HOH700 4.5 39.4 1.0
D2 A:HOH651 4.5 54.8 1.0
O A:HOH713 4.6 41.5 1.0
CG2 A:VAL36 4.7 29.4 1.0
DE2 A:HIS83 4.8 31.9 1.0
HG12 A:VAL36 4.8 31.0 1.0
DD1 A:HIS42 4.8 22.9 1.0
HG23 A:THR122 4.9 24.0 0.3
D2 A:HOH700 5.0 44.8 1.0

Copper binding site 4 out of 4 in 9kvm

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Copper binding site 4 out of 4 in the Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Neutron and X-Ray Joint Refined Structure of A Copper-Containing Nitrite Reductase (C135A Mutant) in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:19.9
occ:0.07
 O A:HOH587 1.5 26.8 0.9
D2 A:HOH587 2.0 30.2 0.9
D1 A:HOH502 2.1 32.7 0.5
D1 A:HOH587 2.2 28.4 0.9
O A:HOH502 2.4 24.3 0.5
O A:HOH502 2.6 32.4 0.5
HD2 A:HIS100 2.7 25.4 1.0
D1 A:HOH502 2.7 21.4 0.5
CD2 A:HIS100 2.9 21.0 1.0
NE2 A:HIS100 3.2 21.2 1.0
D2 A:HOH502 3.2 30.6 0.5
HA A:HIS100 3.4 19.2 1.0
OD1 A:ASP98 3.6 24.0 1.0
CG A:HIS100 3.6 21.2 1.0
CU A:CU402 3.7 22.7 1.0
O A:HOH580 3.8 32.1 1.0
OD2 A:ASP98 3.8 25.5 1.0
CE1 A:HIS100 4.0 20.2 1.0
CG A:ASP98 4.2 23.3 1.0
ND1 A:HIS100 4.2 21.2 1.0
CA A:HIS100 4.3 20.9 1.0
D2 A:HOH580 4.3 35.4 1.0
O A:HOH583 4.3 25.9 1.0
D2 A:HOH583 4.3 24.8 1.0
D1 A:HOH580 4.4 31.0 1.0
CB A:HIS100 4.4 20.1 1.0
D1 A:HOH583 4.4 29.2 1.0
O A:HOH691 4.5 28.2 0.1
O1 A:FMT405 4.5 41.7 0.5
HE2 A:PHE110 4.5 27.1 1.0
HB3 A:HIS100 4.6 22.4 1.0
HE1 A:HIS100 4.6 16.8 1.0
D2 A:HOH691 4.8 27.9 0.1
N A:HIS100 4.9 20.1 1.0
DD1 A:HIS100 5.0 18.1 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 10:03:17 2025

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