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Copper in PDB 7aq3: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D, PDB code: 7aq3 was solved by L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.33 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.664, 76.608, 109.087, 90, 93.26, 90
R / Rfree (%) 15.6 / 19.9

Other elements in 7aq3:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D (pdb code 7aq3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D, PDB code: 7aq3:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 7aq3

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Copper binding site 1 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu707

b:37.5
occ:0.70
 CU1 A:CUA707 0.0 37.5 0.7
SG A:CYS618 2.4 29.3 1.0
SD A:MET629 2.4 26.9 0.7
SG A:CYS622 2.5 25.9 0.7
CU2 A:CUA707 2.7 35.1 0.7
CB A:CYS618 3.2 27.9 1.0
CB A:CYS622 3.4 36.1 1.0
CE A:MET629 3.4 30.0 1.0
OD1 A:ASP583 3.7 45.1 1.0
CG A:MET629 3.8 28.5 1.0
O A:TRP620 3.9 30.4 1.0
CG A:ASP583 4.1 38.6 1.0
CB A:MET629 4.2 31.9 1.0
CB A:ALA552 4.2 37.8 1.0
CB A:ASP583 4.4 24.3 1.0
CA A:ASP583 4.5 23.4 1.0
CA A:CYS618 4.6 23.7 1.0
CA A:ALA552 4.6 34.9 1.0
ND1 A:HIS626 4.7 39.8 1.0
CA A:CYS622 4.8 40.0 1.0
O A:SER582 4.9 25.9 1.0
OD2 A:ASP583 4.9 41.7 1.0
N A:CYS622 4.9 28.8 1.0
N A:GLY584 5.0 23.7 1.0

Copper binding site 2 out of 8 in 7aq3

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Copper binding site 2 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu707

b:35.1
occ:0.69
 CU2 A:CUA707 0.0 35.1 0.7
ND1 A:HIS626 2.2 39.8 1.0
O A:TRP620 2.4 30.4 1.0
SG A:CYS622 2.6 25.9 0.7
CU1 A:CUA707 2.7 37.5 0.7
SG A:CYS618 2.8 29.3 1.0
CE1 A:HIS626 3.1 37.6 1.0
CG A:HIS626 3.2 36.1 1.0
C A:TRP620 3.4 33.7 1.0
N A:CYS622 3.4 28.8 1.0
CB A:CYS622 3.4 36.1 1.0
CB A:HIS626 3.5 34.4 1.0
CB A:CYS618 3.6 27.9 1.0
CA A:PHE621 3.9 34.8 1.0
CA A:HIS626 3.9 38.5 1.0
C A:PHE621 4.0 34.5 1.0
O A:CYS618 4.0 25.4 1.0
N A:PHE621 4.0 35.5 1.0
CA A:CYS622 4.0 40.0 1.0
NE2 A:HIS626 4.2 38.5 1.0
N A:TRP620 4.3 27.6 1.0
CD2 A:HIS626 4.3 40.0 1.0
O A:HIS626 4.3 34.0 1.0
C A:CYS618 4.3 24.5 1.0
CA A:TRP620 4.4 31.1 1.0
C A:HIS626 4.5 36.3 1.0
SD A:MET629 4.6 26.9 0.7
CA A:CYS618 4.6 23.7 1.0
O A:HOH954 4.8 35.7 1.0
CB A:MET629 4.9 31.9 1.0
C A:CYS622 4.9 41.5 1.0
C A:SER619 5.0 34.3 1.0

Copper binding site 3 out of 8 in 7aq3

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Copper binding site 3 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1909

b:40.7
occ:0.64
 CU1 B:CUZ1909 0.0 40.7 0.6
NE2 B:HIS326 2.1 36.7 1.0
NE2 B:HIS382 2.3 37.0 1.0
S1 B:CUZ1909 2.4 43.0 0.7
O B:HOH2360 2.7 48.7 1.0
CD2 B:HIS326 3.1 37.9 1.0
CE1 B:HIS382 3.1 39.1 1.0
CU3 B:CUZ1909 3.1 26.1 0.6
CE1 B:HIS326 3.1 37.8 1.0
CU4 B:CUZ1909 3.3 35.0 0.6
CD2 B:HIS382 3.4 34.8 1.0
NE2 B:HIS433 3.6 39.0 1.0
CD2 B:HIS433 3.9 38.0 1.0
CE1 B:HIS433 4.2 39.5 1.0
ND2 B:ASN241 4.2 30.8 1.0
CG B:HIS326 4.2 35.7 1.0
ND1 B:HIS326 4.2 36.2 1.0
ND1 B:HIS382 4.3 34.0 1.0
CG B:HIS382 4.4 38.0 1.0
CU2 B:CUZ1909 4.5 32.3 0.4
CG B:HIS433 4.6 35.9 1.0
ND1 B:HIS433 4.8 33.5 1.0
CE2 A:PHE621 4.8 39.0 1.0
OD1 B:ASN241 5.0 32.5 1.0

Copper binding site 4 out of 8 in 7aq3

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Copper binding site 4 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1909

b:32.3
occ:0.42
 CU2 B:CUZ1909 0.0 32.3 0.4
S1 B:CUZ1909 2.2 43.0 0.7
NE2 B:HIS178 2.2 39.8 1.0
CD2 B:HIS129 2.5 32.5 1.0
CU3 B:CUZ1909 2.8 26.1 0.6
CU4 B:CUZ1909 2.8 35.0 0.6
CD2 B:HIS178 3.0 34.2 1.0
CG B:HIS129 3.1 26.9 1.0
CE1 B:HIS178 3.2 38.0 1.0
NE2 B:HIS130 3.3 30.1 1.0
CB B:HIS129 3.5 25.2 1.0
CE1 B:HIS130 3.5 28.7 1.0
O A:HOH1078 3.5 39.8 1.0
NE2 B:HIS129 3.5 31.9 1.0
ND1 B:HIS494 3.9 60.1 1.0
CG B:HIS178 4.1 33.4 1.0
ND1 B:HIS178 4.1 37.8 1.0
ND1 B:HIS129 4.2 33.1 1.0
CG B:HIS494 4.4 56.4 1.0
CE1 B:HIS494 4.4 58.9 1.0
CE1 B:HIS129 4.4 27.6 1.0
CD2 B:HIS130 4.4 27.2 1.0
CU1 B:CUZ1909 4.5 40.7 0.6
ND1 B:HIS130 4.6 29.4 1.0
CB B:HIS494 4.7 44.4 1.0
NE2 B:HIS433 4.9 39.0 1.0
CA B:HIS129 4.9 26.6 1.0
SD A:MET627 5.0 28.3 0.6

Copper binding site 5 out of 8 in 7aq3

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Copper binding site 5 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1909

b:26.1
occ:0.56
 CU3 B:CUZ1909 0.0 26.1 0.6
NE2 B:HIS130 2.2 30.1 1.0
NE2 B:HIS433 2.2 39.0 1.0
S1 B:CUZ1909 2.2 43.0 0.7
CU4 B:CUZ1909 2.8 35.0 0.6
CU2 B:CUZ1909 2.8 32.3 0.4
CD2 B:HIS130 3.0 27.2 1.0
CU1 B:CUZ1909 3.1 40.7 0.6
CE1 B:HIS433 3.1 39.5 1.0
CD2 B:HIS433 3.2 38.0 1.0
CE1 B:HIS130 3.3 28.7 1.0
OD1 B:ASN241 3.9 32.5 1.0
O B:HOH2183 4.1 40.5 1.0
NE2 B:HIS382 4.1 37.0 1.0
O B:HOH2360 4.2 48.7 1.0
CG B:HIS130 4.2 31.2 1.0
CE1 B:HIS382 4.3 39.1 1.0
ND1 B:HIS433 4.3 33.5 1.0
NE2 B:HIS178 4.3 39.8 1.0
CB B:HIS494 4.3 44.4 1.0
CB B:HIS129 4.3 25.2 1.0
CG B:HIS433 4.3 35.9 1.0
ND1 B:HIS130 4.3 29.4 1.0
CE1 B:HIS178 4.5 38.0 1.0
ND2 B:ASN241 4.6 30.8 1.0
CG B:ASN241 4.6 33.7 1.0
CD2 B:HIS129 4.6 32.5 1.0
NE2 B:HIS326 4.7 36.7 1.0
ND1 B:HIS494 4.7 60.1 1.0
CG B:HIS494 4.8 56.4 1.0
CG B:HIS129 4.8 26.9 1.0
O B:HIS129 5.0 24.6 1.0

Copper binding site 6 out of 8 in 7aq3

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Copper binding site 6 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1909

b:35.0
occ:0.55
 CU4 B:CUZ1909 0.0 35.0 0.6
S1 B:CUZ1909 2.3 43.0 0.7
ND1 B:HIS494 2.4 60.1 1.0
O B:HOH2360 2.6 48.7 1.0
CU3 B:CUZ1909 2.8 26.1 0.6
CU2 B:CUZ1909 2.8 32.3 0.4
CG B:HIS494 3.0 56.4 1.0
CB B:HIS494 3.1 44.4 1.0
CU1 B:CUZ1909 3.3 40.7 0.6
CE1 B:HIS494 3.5 58.9 1.0
O A:HOH1078 3.6 39.8 1.0
CD2 B:HIS433 3.7 38.0 1.0
CD2 B:HIS129 3.7 32.5 1.0
NE2 B:HIS433 3.8 39.0 1.0
CD2 B:HIS494 4.2 58.7 1.0
CA B:HIS494 4.2 37.7 1.0
NE2 B:HIS494 4.4 58.5 1.0
CE2 A:PHE621 4.4 39.0 1.0
NZ B:LYS454 4.5 31.1 1.0
NE2 B:HIS130 4.5 30.1 1.0
CG B:HIS129 4.5 26.9 1.0
CD2 A:PHE621 4.6 36.3 1.0
CB B:HIS129 4.7 25.2 1.0
NE2 B:HIS178 4.8 39.8 1.0
NE2 B:HIS129 4.8 31.9 1.0
O B:HOH2173 4.9 29.6 1.0
C B:HIS494 4.9 30.5 1.0
CE B:LYS454 5.0 38.7 1.0

Copper binding site 7 out of 8 in 7aq3

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Copper binding site 7 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1910

b:67.6
occ:0.49
 CU1 B:CUA1910 0.0 67.6 0.5
SG B:CYS618 2.6 28.1 0.9
SD B:MET629 2.7 31.5 0.8
SG B:CYS622 2.7 65.6 0.5
CU2 B:CUA1910 2.7 63.7 0.8
CB B:CYS622 3.1 65.9 1.0
OD1 B:ASP583 3.2 36.6 1.0
CE B:MET629 3.6 32.5 1.0
CB B:CYS618 3.6 23.1 1.0
CG B:ASP583 3.8 34.3 1.0
CB B:ALA552 3.9 45.8 1.0
O B:TRP620 4.0 42.4 1.0
CA B:ASP583 4.0 22.6 1.0
CB B:ASP583 4.1 23.5 1.0
CG B:MET629 4.2 31.6 1.0
O B:SER582 4.5 33.7 1.0
CA B:CYS622 4.5 70.1 1.0
CA B:ALA552 4.6 47.0 1.0
CB B:MET629 4.6 31.5 1.0
N B:GLY584 4.7 26.8 1.0
OD2 B:ASP583 4.8 29.9 1.0
O B:HOH2003 4.8 56.9 1.0
N B:CYS622 4.8 56.5 1.0
N B:ASP583 5.0 27.4 1.0
C B:ASP583 5.0 26.5 1.0

Copper binding site 8 out of 8 in 7aq3

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Copper binding site 8 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1910

b:63.7
occ:0.79
 CU2 B:CUA1910 0.0 63.7 0.8
ND1 B:HIS626 2.4 74.3 1.0
SG B:CYS618 2.7 28.1 0.9
CU1 B:CUA1910 2.7 67.6 0.5
SG B:CYS622 2.9 65.6 0.5
O B:TRP620 3.2 42.4 1.0
CE1 B:HIS626 3.3 75.1 1.0
CG B:HIS626 3.4 77.6 1.0
CB B:CYS622 3.4 65.9 1.0
CB B:CYS618 3.5 23.1 1.0
N B:CYS622 3.6 56.5 1.0
CB B:HIS626 3.7 85.6 1.0
O B:CYS618 3.9 26.5 1.0
C B:TRP620 3.9 52.4 1.0
CA B:PHE621 4.0 73.6 1.0
CA B:HIS626 4.1 94.4 1.0
O B:HIS626 4.1 90.9 1.0
C B:PHE621 4.1 63.2 1.0
CA B:CYS622 4.1 70.1 1.0
C B:CYS618 4.3 22.3 1.0
N B:PHE621 4.3 62.1 1.0
SD B:MET629 4.4 31.5 0.8
NE2 B:HIS626 4.4 76.0 1.0
C B:HIS626 4.5 95.8 1.0
CA B:CYS618 4.5 20.8 1.0
CD2 B:HIS626 4.5 76.3 1.0
CB B:MET629 4.6 31.5 1.0
O B:HOH2090 4.7 38.3 1.0
N B:TRP620 4.8 26.8 1.0
C B:CYS622 5.0 90.0 1.0
C B:SER619 5.0 34.5 1.0

Reference:

L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle. Histidine-Gated Proton-Coupled Electron Transfer to the Cu A Site of Nitrous Oxide Reductase. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 33377777
DOI: 10.1021/JACS.0C10057
Page generated: Wed Jul 31 08:14:01 2024

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