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Copper in PDB 7aq8: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A, PDB code: 7aq8 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) 69.43 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.545, 76.667, 109.062, 90, 93.27, 90
R / Rfree (%) 15.8 / 21.7

Other elements in 7aq8:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A also contains other interesting chemical elements:

Potassium (K) 2 atoms
Calcium (Ca) 2 atoms
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, H583Y/D576A (pdb code 7aq8). 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, H583Y/D576A, PDB code: 7aq8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 7aq8

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Copper binding site 1 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu710

b:38.0
occ:0.79
 CU1 A:CUA710 0.0 38.0 0.8
SG A:CYS618 2.3 25.5 0.8
SD A:MET629 2.5 28.3 0.8
SG A:CYS622 2.5 27.4 0.6
CU2 A:CUA710 2.7 55.8 0.9
CB A:CYS618 3.1 28.0 1.0
CE A:MET629 3.3 21.2 1.0
CB A:CYS622 3.4 28.0 1.0
CD1 A:TYR583 3.8 33.0 1.0
CG A:MET629 3.8 33.2 1.0
O A:TRP620 3.9 35.2 1.0
CB A:MET629 4.2 29.8 1.0
CG A:TYR583 4.3 31.6 1.0
CB A:TYR583 4.4 26.1 1.0
CE1 A:TYR583 4.4 35.9 1.0
CA A:CYS618 4.6 29.0 1.0
CB A:ALA552 4.6 36.1 1.0
ND1 A:HIS626 4.6 40.9 1.0
CA A:CYS622 4.6 37.0 1.0
CA A:TYR583 4.6 28.4 1.0
N A:CYS622 4.7 28.1 1.0

Copper binding site 2 out of 8 in 7aq8

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Copper binding site 2 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu710

b:55.8
occ:0.87
 CU2 A:CUA710 0.0 55.8 0.9
ND1 A:HIS626 2.2 40.9 1.0
O A:TRP620 2.6 35.2 1.0
CU1 A:CUA710 2.7 38.0 0.8
SG A:CYS622 2.7 27.4 0.6
N A:CYS622 3.0 28.1 1.0
CG A:HIS626 3.0 39.2 1.0
CB A:HIS626 3.2 34.0 1.0
CE1 A:HIS626 3.2 42.7 1.0
SG A:CYS618 3.3 25.5 0.8
CB A:CYS622 3.3 28.0 1.0
C A:TRP620 3.5 33.9 1.0
CA A:HIS626 3.6 35.5 1.0
CA A:PHE621 3.6 41.2 1.0
CA A:CYS622 3.7 37.0 1.0
C A:PHE621 3.7 39.3 1.0
N A:PHE621 4.0 39.2 1.0
CB A:CYS618 4.1 28.0 1.0
CD2 A:HIS626 4.2 43.9 1.0
O A:HIS626 4.2 28.9 1.0
NE2 A:HIS626 4.2 43.1 1.0
C A:HIS626 4.3 38.8 1.0
O A:CYS618 4.4 27.1 1.0
C A:CYS622 4.5 41.8 1.0
N A:HIS623 4.5 42.7 1.0
SD A:MET629 4.6 28.3 0.8
N A:TRP620 4.7 29.1 1.0
CA A:TRP620 4.7 34.7 1.0
N A:HIS626 4.8 31.5 1.0
C A:CYS618 4.8 27.7 1.0
O A:PHE621 4.8 34.9 1.0
O A:HOH952 4.9 41.3 1.0

Copper binding site 3 out of 8 in 7aq8

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Copper binding site 3 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:44.3
occ:0.56
 CU1 B:CUZ708 0.0 44.3 0.6
NE2 B:HIS326 2.2 40.2 1.0
NE2 B:HIS382 2.3 53.7 1.0
S1 B:CUZ708 2.4 54.2 0.9
O B:HOH1086 2.9 48.0 1.0
CD2 B:HIS326 3.0 38.5 1.0
NE2 B:HIS433 3.1 44.7 1.0
CU3 B:CUZ708 3.3 34.6 0.6
CE1 B:HIS382 3.3 56.7 1.0
CE1 B:HIS326 3.3 35.9 1.0
CD2 B:HIS382 3.3 56.6 1.0
CU4 B:CUZ708 3.3 50.0 0.7
CD2 B:HIS433 3.5 40.3 1.0
CE1 B:HIS433 4.0 41.0 1.0
CG B:HIS326 4.2 35.9 1.0
ND2 B:ASN241 4.2 40.5 1.0
ND1 B:HIS326 4.3 42.1 1.0
ND1 B:HIS382 4.4 59.3 1.0
CG B:HIS382 4.5 53.1 1.0
CG B:HIS433 4.5 41.1 1.0
CU2 B:CUZ708 4.6 42.2 0.5
ND1 B:HIS433 4.7 31.8 1.0
CE2 A:PHE621 4.8 39.3 1.0

Copper binding site 4 out of 8 in 7aq8

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Copper binding site 4 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:42.2
occ:0.46
 CU2 B:CUZ708 0.0 42.2 0.5
S1 B:CUZ708 2.2 54.2 0.9
NE2 B:HIS178 2.2 43.6 1.0
CD2 B:HIS129 2.5 36.5 1.0
CU3 B:CUZ708 2.8 34.6 0.6
CU4 B:CUZ708 2.8 50.0 0.7
CD2 B:HIS178 3.0 39.6 1.0
CG B:HIS129 3.1 29.9 1.0
CE1 B:HIS178 3.2 36.9 1.0
CB B:HIS129 3.4 23.8 1.0
NE2 B:HIS130 3.4 32.2 1.0
NE2 B:HIS129 3.6 33.0 1.0
CE1 B:HIS130 3.7 28.3 1.0
CD2 B:HIS494 3.9 64.5 1.0
CG B:HIS178 4.1 39.4 1.0
ND1 B:HIS178 4.2 42.1 1.0
CG B:HIS494 4.2 62.3 1.0
ND1 B:HIS129 4.2 33.3 1.0
CE1 B:HIS129 4.4 31.8 1.0
CD2 B:HIS130 4.5 33.8 1.0
NE2 B:HIS494 4.5 65.2 1.0
CB B:HIS494 4.5 48.2 1.0
CU1 B:CUZ708 4.6 44.3 0.6
NE2 B:HIS433 4.7 44.7 1.0
ND1 B:HIS130 4.8 35.4 1.0
CA B:HIS129 4.8 25.0 1.0
ND1 B:HIS494 4.9 69.2 1.0

Copper binding site 5 out of 8 in 7aq8

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Copper binding site 5 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:34.6
occ:0.61
 CU3 B:CUZ708 0.0 34.6 0.6
NE2 B:HIS433 2.2 44.7 1.0
NE2 B:HIS130 2.2 32.2 1.0
S1 B:CUZ708 2.2 54.2 0.9
CU2 B:CUZ708 2.8 42.2 0.5
CU4 B:CUZ708 2.9 50.0 0.7
CD2 B:HIS130 2.9 33.8 1.0
CE1 B:HIS433 2.9 41.0 1.0
CU1 B:CUZ708 3.3 44.3 0.6
CD2 B:HIS433 3.3 40.3 1.0
CE1 B:HIS130 3.3 28.3 1.0
OD1 B:ASN241 3.8 52.1 1.0
O B:HOH821 4.1 56.5 1.0
NE2 B:HIS382 4.1 53.7 1.0
ND1 B:HIS433 4.1 31.8 1.0
CB B:HIS129 4.1 23.8 1.0
CG B:HIS130 4.2 37.4 1.0
NE2 B:HIS178 4.2 43.6 1.0
CB B:HIS494 4.2 48.2 1.0
ND1 B:HIS130 4.3 35.4 1.0
CG B:HIS433 4.3 41.1 1.0
O B:HOH1086 4.3 48.0 1.0
CE1 B:HIS382 4.3 56.7 1.0
CE1 B:HIS178 4.4 36.9 1.0
ND2 B:ASN241 4.6 40.5 1.0
CG B:ASN241 4.6 39.0 1.0
CD2 B:HIS129 4.7 36.5 1.0
NE2 B:HIS326 4.7 40.2 1.0
CG B:HIS494 4.8 62.3 1.0
CG B:HIS129 4.8 29.9 1.0
O B:HIS129 4.8 33.2 1.0
CD2 B:HIS494 5.0 64.5 1.0

Copper binding site 6 out of 8 in 7aq8

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Copper binding site 6 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:50.0
occ:0.71
 CU4 B:CUZ708 0.0 50.0 0.7
S1 B:CUZ708 2.4 54.2 0.9
O B:HOH1086 2.5 48.0 1.0
CD2 B:HIS494 2.5 64.5 1.0
CU2 B:CUZ708 2.8 42.2 0.5
CU3 B:CUZ708 2.9 34.6 0.6
CG B:HIS494 2.9 62.3 1.0
CB B:HIS494 2.9 48.2 1.0
CU1 B:CUZ708 3.3 44.3 0.6
NE2 B:HIS433 3.5 44.7 1.0
CD2 B:HIS433 3.6 40.3 1.0
NE2 B:HIS494 3.8 65.2 1.0
CD2 B:HIS129 3.9 36.5 1.0
CA B:HIS494 4.1 39.7 1.0
ND1 B:HIS494 4.2 69.2 1.0
NZ B:LYS454 4.4 38.0 1.0
CE2 A:PHE621 4.5 39.3 1.0
CE1 B:HIS494 4.6 67.6 1.0
CG B:HIS129 4.6 29.9 1.0
CD2 A:PHE621 4.6 41.4 1.0
CB B:HIS129 4.6 23.8 1.0
O B:HOH847 4.7 29.9 1.0
NE2 B:HIS130 4.7 32.2 1.0
CE1 B:HIS433 4.8 41.0 1.0
C B:HIS494 4.8 34.0 1.0
NE2 B:HIS178 4.8 43.6 1.0
CG B:HIS433 4.9 41.1 1.0
CE B:LYS454 5.0 35.5 1.0
NE2 B:HIS129 5.0 33.0 1.0

Copper binding site 7 out of 8 in 7aq8

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Copper binding site 7 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:47.5
occ:0.56
 CU1 B:CUA709 0.0 47.5 0.6
SG B:CYS618 2.5 36.8 1.0
SG B:CYS622 2.6 49.2 0.6
SD B:MET629 2.6 38.5 0.7
CU2 B:CUA709 2.7 77.9 1.0
CB B:CYS618 3.2 26.1 1.0
CG B:MET629 3.7 38.5 1.0
CE B:MET629 3.7 37.2 1.0
CB B:CYS622 3.7 57.9 1.0
CD1 B:TYR583 3.8 44.2 1.0
CB B:MET629 3.9 32.6 1.0
O B:TRP620 4.1 57.8 1.0
CE1 B:TYR583 4.5 41.6 1.0
CG B:TYR583 4.5 35.2 1.0
CB B:TYR583 4.6 32.2 1.0
CB B:ALA552 4.6 47.3 1.0
CA B:CYS618 4.6 31.5 1.0
CD2 B:HIS626 4.7 79.2 1.0
CA B:TYR583 4.8 27.8 1.0
CA B:CYS622 4.9 69.2 1.0
N B:CYS622 4.9 57.9 1.0

Copper binding site 8 out of 8 in 7aq8

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Copper binding site 8 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:77.9
occ:0.96
 CU2 B:CUA709 0.0 77.9 1.0
CD2 B:HIS626 2.5 79.2 1.0
CU1 B:CUA709 2.7 47.5 0.6
O B:TRP620 2.7 57.8 1.0
CG B:HIS626 3.0 77.4 1.0
SG B:CYS622 3.0 49.2 0.6
N B:CYS622 3.1 57.9 1.0
SG B:CYS618 3.1 36.8 1.0
CB B:HIS626 3.3 77.9 1.0
NE2 B:HIS626 3.5 79.2 1.0
C B:TRP620 3.6 56.8 1.0
CB B:CYS622 3.6 57.9 1.0
CA B:PHE621 3.6 65.8 1.0
C B:PHE621 3.7 67.9 1.0
CA B:HIS626 3.8 85.5 1.0
CA B:CYS622 3.9 69.2 1.0
N B:PHE621 3.9 65.5 1.0
ND1 B:HIS626 4.0 82.9 1.0
O B:HIS626 4.1 63.3 1.0
CB B:CYS618 4.2 26.1 1.0
O B:CYS618 4.2 30.2 1.0
CE1 B:HIS626 4.2 82.4 1.0
C B:HIS626 4.3 79.7 1.0
N B:HIS623 4.6 85.8 1.0
C B:CYS622 4.7 80.8 1.0
C B:CYS618 4.7 27.8 1.0
N B:TRP620 4.7 39.1 1.0
CA B:TRP620 4.7 45.5 1.0
O B:PHE621 4.8 72.2 1.0
O B:HOH825 4.8 38.7 1.0
C B:SER619 5.0 36.2 1.0
CB B:PHE621 5.0 58.0 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 08:14:43 2024

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