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Copper in PDB 7aqa: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A, PDB code: 7aqa 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) 62.67 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.824, 76.834, 108.513, 90, 93.47, 90
R / Rfree (%) 15.6 / 19.4

Other elements in 7aqa:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 1 atom
Potassium (K) 2 atoms
Chlorine (Cl) 3 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Copper atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A (pdb code 7aqa). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 11 binding sites of Copper where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A, PDB code: 7aqa:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 11 in 7aqa

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Copper binding site 1 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:67.1
occ:0.42
 CU1 A:K7E701 0.0 67.1 0.4
NE2 A:HIS326 2.2 20.3 1.0
S1 A:K7E701 2.3 26.9 0.6
CE1 A:HIS433 2.4 43.9 1.0
S2 A:K7E701 2.8 29.1 0.6
ND1 A:HIS433 3.0 43.3 1.0
CU4 A:K7E701 3.0 28.6 0.5
CE1 A:HIS326 3.0 19.8 1.0
CD2 A:HIS326 3.3 19.0 1.0
CU3 A:K7E701 3.4 21.1 0.4
NE2 A:HIS433 3.5 45.2 1.0
CG A:HIS433 4.2 37.3 1.0
ND1 A:HIS326 4.2 19.6 1.0
CG A:HIS326 4.3 18.1 1.0
CU2 A:K7E701 4.4 17.1 0.3
CD2 A:HIS433 4.4 41.6 1.0
CE2 B:PHE621 4.5 34.7 1.0
ND2 A:ASN241 4.5 33.1 1.0
O B:HOH1175 4.8 31.6 1.0

Copper binding site 2 out of 11 in 7aqa

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Copper binding site 2 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:17.1
occ:0.28
 CU2 A:K7E701 0.0 17.1 0.3
NE2 A:HIS178 2.0 26.4 1.0
S1 A:K7E701 2.2 26.9 0.6
ND1 A:HIS129 2.6 22.7 1.0
CD2 A:HIS178 2.7 25.8 1.0
CU3 A:K7E701 2.8 21.1 0.4
CU4 A:K7E701 2.8 28.6 0.5
CG A:HIS129 3.1 19.0 1.0
CE1 A:HIS178 3.1 28.7 1.0
NE2 A:HIS130 3.3 21.9 1.0
O B:HOH1175 3.3 31.6 1.0
CB A:HIS129 3.4 20.3 1.0
CE1 A:HIS129 3.4 21.6 1.0
CE1 A:HIS130 3.4 18.2 1.0
CG A:HIS178 3.9 25.4 1.0
ND1 A:HIS494 3.9 53.2 1.0
CD2 A:HIS129 4.0 24.3 1.0
ND1 A:HIS178 4.0 26.7 1.0
NE2 A:HIS129 4.2 27.5 1.0
CU1 A:K7E701 4.4 67.1 0.4
CD2 A:HIS130 4.4 18.1 1.0
ND1 A:HIS130 4.5 17.9 1.0
CE B:MET627 4.6 46.8 1.0
CG A:HIS494 4.6 47.3 1.0
CE1 A:HIS494 4.6 51.8 1.0
CB A:HIS494 4.8 38.7 1.0
CA A:HIS129 4.8 21.8 1.0
SD B:MET627 4.8 61.7 0.7
OD1 A:ASN241 4.9 34.0 1.0

Copper binding site 3 out of 11 in 7aqa

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Copper binding site 3 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:21.1
occ:0.37
 CU3 A:K7E701 0.0 21.1 0.4
NE2 A:HIS130 2.1 21.9 1.0
S1 A:K7E701 2.2 26.9 0.6
NE2 A:HIS433 2.6 45.2 1.0
CU4 A:K7E701 2.8 28.6 0.5
CD2 A:HIS130 2.8 18.1 1.0
CU2 A:K7E701 2.8 17.1 0.3
CE1 A:HIS433 3.0 43.9 1.0
CE1 A:HIS130 3.2 18.2 1.0
CU1 A:K7E701 3.4 67.1 0.4
CD2 A:HIS433 3.4 41.6 1.0
OD1 A:ASN241 3.9 34.0 1.0
ND1 A:HIS433 3.9 43.3 1.0
O A:HOH1123 4.0 36.7 1.0
CB A:HIS129 4.0 20.3 1.0
CG A:HIS130 4.0 18.2 1.0
NE2 A:HIS178 4.1 26.4 1.0
CG A:HIS433 4.1 37.3 1.0
ND1 A:HIS130 4.2 17.9 1.0
CB A:HIS494 4.2 38.7 1.0
ND2 A:ASN241 4.3 33.1 1.0
S2 A:K7E701 4.4 29.1 0.6
CE1 A:HIS178 4.5 28.7 1.0
CG A:ASN241 4.5 28.8 1.0
ND1 A:HIS129 4.6 22.7 1.0
NE2 A:HIS326 4.6 20.3 1.0
O A:HIS129 4.7 18.8 1.0
CG A:HIS129 4.7 19.0 1.0
ND1 A:HIS494 4.9 53.2 1.0
CE1 A:HIS326 4.9 19.8 1.0
C A:HIS129 4.9 20.1 1.0
CG A:HIS494 5.0 47.3 1.0
CD2 A:HIS178 5.0 25.8 1.0

Copper binding site 4 out of 11 in 7aqa

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Copper binding site 4 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:28.6
occ:0.52
 CU4 A:K7E701 0.0 28.6 0.5
S1 A:K7E701 2.3 26.9 0.6
S2 A:K7E701 2.3 29.1 0.6
ND1 A:HIS494 2.6 53.2 1.0
CU3 A:K7E701 2.8 21.1 0.4
CB A:HIS494 2.8 38.7 1.0
CU2 A:K7E701 2.8 17.1 0.3
CU1 A:K7E701 3.0 67.1 0.4
CG A:HIS494 3.0 47.3 1.0
O B:HOH1175 3.5 31.6 1.0
ND1 A:HIS129 3.6 22.7 1.0
CE1 A:HIS494 3.8 51.8 1.0
CE1 A:HIS433 4.1 43.9 1.0
CA A:HIS494 4.1 35.1 1.0
CB A:HIS129 4.3 20.3 1.0
CD2 A:HIS494 4.3 50.3 1.0
ND1 A:HIS433 4.4 43.3 1.0
CG A:HIS129 4.4 19.0 1.0
NE2 A:HIS433 4.4 45.2 1.0
NE2 A:HIS130 4.4 21.9 1.0
NZ A:LYS454 4.6 27.4 1.0
CE1 A:HIS129 4.6 21.6 1.0
NE2 A:HIS178 4.6 26.4 1.0
NE2 A:HIS494 4.7 44.7 1.0
C A:HIS494 4.8 25.0 1.0
CG A:HIS433 4.9 37.3 1.0
CD2 A:HIS433 4.9 41.6 1.0
NE2 A:HIS326 5.0 20.3 1.0
CE2 B:PHE621 5.0 34.7 1.0

Copper binding site 5 out of 11 in 7aqa

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Copper binding site 5 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:31.9
occ:1.00
 CU1 A:CUA708 0.0 31.9 1.0
SG A:CYS618 2.4 16.4 0.8
SD A:MET629 2.4 22.9 1.0
SG A:CYS622 2.5 25.3 1.0
CU2 A:CUA708 2.6 33.5 1.0
CB A:CYS618 3.2 23.6 1.0
CE A:MET629 3.3 23.5 1.0
CB A:CYS622 3.4 23.3 1.0
CD2 A:HIS583 3.7 31.8 1.0
CG A:MET629 3.7 21.1 1.0
O A:TRP620 3.9 18.9 1.0
CG A:HIS583 4.0 24.8 1.0
CB A:HIS583 4.0 17.0 1.0
CB A:MET629 4.2 20.5 1.0
CA A:HIS583 4.2 17.4 1.0
CA A:CYS618 4.6 16.9 1.0
NE2 A:HIS583 4.6 27.0 1.0
O A:SER582 4.7 20.3 1.0
ND1 A:HIS626 4.7 29.5 1.0
CA A:CYS622 4.8 25.8 1.0
N A:GLY584 4.9 17.8 1.0
N A:CYS622 4.9 26.1 1.0
CB A:ALA552 4.9 30.8 1.0
ND1 A:HIS583 5.0 30.6 1.0

Copper binding site 6 out of 11 in 7aqa

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Copper binding site 6 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:33.5
occ:1.00
 CU2 A:CUA708 0.0 33.5 1.0
ND1 A:HIS626 2.1 29.5 1.0
O A:TRP620 2.5 18.9 1.0
SG A:CYS622 2.6 25.3 1.0
CU1 A:CUA708 2.6 31.9 1.0
SG A:CYS618 2.8 16.4 0.8
CG A:HIS626 3.1 30.4 1.0
CE1 A:HIS626 3.1 33.3 1.0
N A:CYS622 3.3 26.1 1.0
CB A:HIS626 3.4 24.7 1.0
C A:TRP620 3.4 21.9 1.0
CB A:CYS622 3.4 23.3 1.0
CB A:CYS618 3.6 23.6 1.0
CA A:HIS626 3.8 25.6 1.0
CA A:PHE621 3.9 22.2 1.0
C A:PHE621 4.0 28.7 1.0
CA A:CYS622 4.0 25.8 1.0
O A:CYS618 4.0 19.8 1.0
N A:PHE621 4.0 26.7 1.0
O A:HIS626 4.2 26.6 1.0
NE2 A:HIS626 4.2 34.0 1.0
CD2 A:HIS626 4.2 33.1 1.0
N A:TRP620 4.3 18.9 1.0
C A:CYS618 4.4 19.1 1.0
SD A:MET629 4.4 22.9 1.0
C A:HIS626 4.4 24.3 1.0
CA A:TRP620 4.5 17.6 1.0
CA A:CYS618 4.7 16.9 1.0
CB A:MET629 4.7 20.5 1.0
C A:CYS622 4.8 26.8 1.0
O A:HOH933 4.9 29.3 1.0
N A:HIS623 4.9 24.8 1.0

Copper binding site 7 out of 11 in 7aqa

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Copper binding site 7 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:24.2
occ:0.39
 CU2 B:RUQ702 0.0 24.2 0.4
NE2 B:HIS178 1.9 30.2 1.0
S1 B:RUQ702 2.2 29.3 0.7
ND1 B:HIS129 2.6 33.7 1.0
CD2 B:HIS178 2.7 29.8 1.0
CU4 B:RUQ702 2.8 31.9 0.5
CU3 B:RUQ702 2.8 26.8 0.5
CE1 B:HIS178 2.9 29.6 1.0
CG B:HIS129 3.4 21.4 1.0
CE1 B:HIS129 3.4 29.8 1.0
NE2 B:HIS130 3.4 25.8 1.0
CE1 B:HIS130 3.5 25.0 1.0
O A:HOH1055 3.6 35.0 1.0
CB B:HIS129 3.7 22.6 1.0
ND1 B:HIS494 3.8 48.7 1.0
CG B:HIS178 3.9 24.0 1.0
ND1 B:HIS178 3.9 33.5 1.0
CD2 B:HIS129 4.3 23.8 1.0
NE2 B:HIS129 4.3 28.9 1.0
CE1 B:HIS494 4.4 46.0 1.0
CD2 B:HIS130 4.6 22.8 1.0
CG B:HIS494 4.6 41.3 1.0
ND1 B:HIS130 4.6 21.7 1.0
OD1 B:ASN241 4.8 38.5 1.0
SD A:MET627 4.9 28.0 0.7
CB B:HIS494 4.9 32.3 1.0
S2 B:RUQ702 5.0 39.1 0.8
CE A:MET627 5.0 34.6 1.0
CE1 B:HIS326 5.0 28.7 1.0

Copper binding site 8 out of 11 in 7aqa

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Copper binding site 8 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


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, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:26.8
occ:0.49
 CU3 B:RUQ702 0.0 26.8 0.5
NE2 B:HIS130 2.1 25.8 1.0
S1 B:RUQ702 2.2 29.3 0.7
NE2 B:HIS433 2.6 47.7 1.0
CU2 B:RUQ702 2.8 24.2 0.4
CE1 B:HIS433 2.8 45.9 1.0
CU4 B:RUQ702 2.9 31.9 0.5
CD2 B:HIS130 3.0 22.8 1.0
CE1 B:HIS130 3.1 25.0 1.0
CD2 B:HIS433 3.7 47.3 1.0
OD1 B:ASN241 3.7 38.5 1.0
ND1 B:HIS433 3.8 42.9 1.0
NE2 B:HIS178 4.0 30.2 1.0
O B:HOH1134 4.0 38.8 1.0
CG B:HIS130 4.1 23.4 1.0
ND2 B:ASN241 4.2 31.5 1.0
ND1 B:HIS130 4.2 21.7 1.0
CB B:HIS129 4.2 22.6 1.0
CG B:HIS433 4.2 38.6 1.0
CE1 B:HIS178 4.3 29.6 1.0
CG B:ASN241 4.3 27.8 1.0
S2 B:RUQ702 4.3 39.1 0.8
CB B:HIS494 4.4 32.3 1.0
NE2 B:HIS326 4.4 29.1 1.0
ND1 B:HIS129 4.6 33.7 1.0
ND1 B:HIS494 4.6 48.7 1.0
CE1 B:HIS326 4.7 28.7 1.0
CG B:HIS129 4.8 21.4 1.0
CD2 B:HIS178 4.9 29.8 1.0
CG B:HIS494 4.9 41.3 1.0
O B:HIS129 5.0 23.0 1.0

Copper binding site 9 out of 11 in 7aqa

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Copper binding site 9 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:31.9
occ:0.54
 CU4 B:RUQ702 0.0 31.9 0.5
ND1 B:HIS494 2.2 48.7 1.0
S1 B:RUQ702 2.3 29.3 0.7
S2 B:RUQ702 2.3 39.1 0.8
CU2 B:RUQ702 2.8 24.2 0.4
CU3 B:RUQ702 2.9 26.8 0.5
CG B:HIS494 3.0 41.3 1.0
CB B:HIS494 3.0 32.3 1.0
CE1 B:HIS494 3.3 46.0 1.0
ND1 B:HIS129 3.5 33.7 1.0
O A:HOH1055 3.5 35.0 1.0
CD2 B:HIS494 4.2 42.4 1.0
CE1 B:HIS433 4.3 45.9 1.0
CA B:HIS494 4.3 25.2 1.0
NE2 B:HIS494 4.3 40.8 1.0
CB B:HIS129 4.4 22.6 1.0
CG B:HIS129 4.4 21.4 1.0
CE1 B:HIS129 4.4 29.8 1.0
NZ B:LYS454 4.5 26.4 1.0
ND1 B:HIS433 4.5 42.9 1.0
NE2 B:HIS178 4.5 30.2 1.0
NE2 B:HIS130 4.6 25.8 1.0
NE2 B:HIS433 4.7 47.7 1.0
CE2 A:PHE621 4.8 25.3 1.0
CD2 A:PHE621 4.9 29.5 1.0
NE2 B:HIS326 5.0 29.1 1.0

Copper binding site 10 out of 11 in 7aqa

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Copper binding site 10 out of 11 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H382A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:35.5
occ:1.00
 CU1 B:CUA708 0.0 35.5 1.0
SG B:CYS618 2.4 21.1 1.0
SD B:MET629 2.5 27.9 1.0
SG B:CYS622 2.5 18.0 0.7
CU2 B:CUA708 2.7 32.6 0.8
CB B:CYS618 3.2 22.8 1.0
CE B:MET629 3.3 23.0 1.0
CB B:CYS622 3.3 25.0 1.0
CD2 B:HIS583 3.7 35.7 1.0
CG B:MET629 3.8 26.3 1.0
O B:TRP620 3.9 22.3 1.0
CG B:HIS583 4.0 28.2 1.0
CB B:HIS583 4.1 18.7 1.0
CB B:MET629 4.2 25.3 1.0
CA B:HIS583 4.3 20.4 1.0
NE2 B:HIS583 4.6 30.1 1.0
CA B:CYS618 4.6 18.3 1.0
CA B:CYS622 4.7 31.9 1.0
ND1 B:HIS626 4.7 27.4 1.0
O B:SER582 4.7 20.2 1.0
CB B:ALA552 4.8 38.2 1.0
N B:CYS622 4.8 32.1 1.0
N B:GLY584 4.9 15.6 1.0

Reference:

L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle. A [3CU:2S] Cluster Provides Insight Into the Assembly and Function of the Cuz Site of Nitrous Oxide Reductase Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC05204C
Page generated: Wed Jul 31 08:18:23 2024

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