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Copper in PDB 7aq7: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y

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

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y, PDB code: 7aq7 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) 68.61 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.734, 76.071, 108.467, 90, 93.49, 90
R / Rfree (%) 15.2 / 20.4

Other elements in 7aq7:

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

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

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y (pdb code 7aq7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y, PDB code: 7aq7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 7aq7

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Copper binding site 1 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu712

b:39.2
occ:0.41
 CU1 A:CUZ712 0.0 39.2 0.4
NE2 A:HIS326 2.2 30.3 1.0
NE2 A:HIS382 2.4 43.3 1.0
S1 A:CUZ712 2.5 39.6 0.6
CE1 A:HIS326 3.1 31.8 1.0
CD2 A:HIS326 3.1 26.4 1.0
NE2 A:HIS433 3.3 37.2 1.0
CD2 A:HIS382 3.3 43.5 1.0
CU3 A:CUZ712 3.3 29.2 0.6
CD2 A:HIS433 3.3 40.4 1.0
CU4 A:CUZ712 3.4 36.0 0.6
CE1 A:HIS382 3.5 45.6 1.0
O A:HOH839 3.9 35.5 1.0
ND1 A:HIS326 4.2 31.8 1.0
CG A:HIS326 4.3 24.6 1.0
CE1 A:HIS433 4.4 30.9 1.0
CG A:HIS433 4.4 33.1 1.0
CG A:HIS382 4.5 40.0 1.0
ND1 A:HIS382 4.5 39.3 1.0
CU2 A:CUZ712 4.6 21.2 0.2
ND2 A:ASN241 4.6 34.1 1.0
CE2 B:PHE621 4.6 42.0 1.0
ND1 A:HIS433 4.9 32.7 1.0
N A:HIS433 4.9 19.1 1.0

Copper binding site 2 out of 12 in 7aq7

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Copper binding site 2 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu712

b:21.2
occ:0.22
 CU2 A:CUZ712 0.0 21.2 0.2
NE2 A:HIS178 2.2 34.4 1.0
S1 A:CUZ712 2.2 39.6 0.6
CD2 A:HIS129 2.6 23.3 1.0
CU3 A:CUZ712 2.7 29.2 0.6
CU4 A:CUZ712 2.8 36.0 0.6
CD2 A:HIS178 3.0 31.6 1.0
CG A:HIS129 3.1 22.4 1.0
CE1 A:HIS178 3.1 37.3 1.0
O A:HOH1224 3.2 32.6 1.0
NE2 A:HIS130 3.3 23.0 1.0
CB A:HIS129 3.4 18.7 1.0
CE1 A:HIS130 3.5 22.8 1.0
NE2 A:HIS129 3.6 26.8 1.0
ND1 A:HIS494 4.0 77.1 1.0
CG A:HIS178 4.1 34.0 1.0
ND1 A:HIS178 4.1 36.5 1.0
ND1 A:HIS129 4.1 22.4 1.0
CG A:HIS494 4.3 65.5 1.0
CE1 A:HIS129 4.3 26.9 1.0
CD2 A:HIS130 4.4 20.7 1.0
CB A:HIS494 4.5 43.0 1.0
CE1 A:HIS494 4.6 78.4 1.0
CU1 A:CUZ712 4.6 39.2 0.4
ND1 A:HIS130 4.6 22.3 1.0
CA A:HIS129 4.8 21.1 1.0
NE2 A:HIS433 4.8 37.2 1.0
O A:HOH839 4.9 35.5 1.0
SD B:MET627 4.9 54.2 0.8
O A:HOH1023 5.0 30.9 1.0

Copper binding site 3 out of 12 in 7aq7

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Copper binding site 3 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu712

b:29.2
occ:0.58
 CU3 A:CUZ712 0.0 29.2 0.6
S1 A:CUZ712 2.2 39.6 0.6
NE2 A:HIS130 2.2 23.0 1.0
NE2 A:HIS433 2.2 37.2 1.0
CU4 A:CUZ712 2.7 36.0 0.6
CU2 A:CUZ712 2.7 21.2 0.2
CD2 A:HIS433 3.1 40.4 1.0
CD2 A:HIS130 3.1 20.7 1.0
CE1 A:HIS433 3.2 30.9 1.0
CE1 A:HIS130 3.2 22.8 1.0
CU1 A:CUZ712 3.3 39.2 0.4
OD1 A:ASN241 3.9 33.8 1.0
NE2 A:HIS382 4.1 43.3 1.0
NE2 A:HIS178 4.1 34.4 1.0
CB A:HIS129 4.2 18.7 1.0
CG A:HIS433 4.2 33.1 1.0
CG A:HIS130 4.3 22.4 1.0
ND1 A:HIS433 4.3 32.7 1.0
CB A:HIS494 4.3 43.0 1.0
CE1 A:HIS382 4.3 45.6 1.0
ND1 A:HIS130 4.3 22.3 1.0
CE1 A:HIS178 4.3 37.3 1.0
O A:HOH1146 4.4 40.5 1.0
O A:HOH839 4.4 35.5 1.0
NE2 A:HIS326 4.6 30.3 1.0
CD2 A:HIS129 4.7 23.3 1.0
CG A:ASN241 4.7 30.2 1.0
ND2 A:ASN241 4.8 34.1 1.0
CG A:HIS129 4.8 22.4 1.0
O A:HIS129 4.9 25.5 1.0
CG A:HIS494 4.9 65.5 1.0
ND1 A:HIS494 5.0 77.1 1.0
CE1 A:HIS326 5.0 31.8 1.0

Copper binding site 4 out of 12 in 7aq7

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Copper binding site 4 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu712

b:36.0
occ:0.58
 CU4 A:CUZ712 0.0 36.0 0.6
O A:HOH839 2.1 35.5 1.0
S1 A:CUZ712 2.4 39.6 0.6
ND1 A:HIS494 2.5 77.1 1.0
CU3 A:CUZ712 2.7 29.2 0.6
CU2 A:CUZ712 2.8 21.2 0.2
CB A:HIS494 2.8 43.0 1.0
CG A:HIS494 3.0 65.5 1.0
CU1 A:CUZ712 3.4 39.2 0.4
CD2 A:HIS433 3.6 40.4 1.0
O A:HOH1224 3.7 32.6 1.0
CE1 A:HIS494 3.7 78.4 1.0
CD2 A:HIS129 3.8 23.3 1.0
NE2 A:HIS433 3.8 37.2 1.0
CA A:HIS494 4.0 34.3 1.0
CD2 A:HIS494 4.2 75.2 1.0
NZ A:LYS454 4.2 26.6 1.0
NE2 A:HIS130 4.5 23.0 1.0
CG A:HIS129 4.5 22.4 1.0
CB A:HIS129 4.5 18.7 1.0
NE2 A:HIS494 4.5 78.0 1.0
C A:HIS494 4.6 25.5 1.0
NE2 A:HIS178 4.8 34.4 1.0
O A:HIS494 4.8 28.8 1.0
O A:HOH935 4.8 27.7 1.0
CD2 B:PHE621 4.8 39.3 1.0
CG A:HIS433 4.9 33.1 1.0
NE2 A:HIS129 4.9 26.8 1.0
CE2 B:PHE621 4.9 42.0 1.0
CE A:LYS454 4.9 29.6 1.0

Copper binding site 5 out of 12 in 7aq7

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Copper binding site 5 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:27.9
occ:0.76
 CU1 A:CUA713 0.0 27.9 0.8
SG A:CYS618 2.3 22.1 1.0
SD A:MET629 2.4 22.3 0.7
SG A:CYS622 2.4 22.9 0.8
CU2 A:CUA713 2.6 44.0 0.9
CB A:CYS618 3.1 16.4 1.0
CE A:MET629 3.3 25.0 1.0
CB A:CYS622 3.5 26.6 1.0
CG A:MET629 3.6 22.5 1.0
O A:TRP620 3.9 25.9 1.0
CD1 A:TYR583 3.9 25.4 1.0
CB A:MET629 4.0 23.2 1.0
CG A:TYR583 4.4 18.7 1.0
CB A:TYR583 4.5 18.4 1.0
ND1 A:HIS626 4.5 32.8 1.0
CA A:CYS618 4.5 19.2 1.0
CE1 A:TYR583 4.5 25.2 1.0
CA A:TYR583 4.7 18.7 1.0
CB A:ALA552 4.7 30.5 1.0
CA A:CYS622 4.8 26.5 1.0
N A:CYS622 4.9 23.1 1.0
C A:CYS618 5.0 20.1 1.0

Copper binding site 6 out of 12 in 7aq7

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Copper binding site 6 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:44.0
occ:0.86
 CU2 A:CUA713 0.0 44.0 0.9
ND1 A:HIS626 2.2 32.8 1.0
O A:TRP620 2.4 25.9 1.0
SG A:CYS622 2.6 22.9 0.8
CU1 A:CUA713 2.6 27.9 0.8
CG A:HIS626 3.0 36.5 1.0
SG A:CYS618 3.1 22.1 1.0
CE1 A:HIS626 3.1 37.5 1.0
N A:CYS622 3.1 23.1 1.0
CB A:HIS626 3.3 33.2 1.0
CB A:CYS622 3.3 26.6 1.0
C A:TRP620 3.4 27.9 1.0
CA A:PHE621 3.6 24.0 1.0
CA A:HIS626 3.7 31.5 1.0
C A:PHE621 3.7 31.0 1.0
CA A:CYS622 3.8 26.5 1.0
N A:PHE621 3.9 31.1 1.0
CB A:CYS618 4.0 16.4 1.0
CD2 A:HIS626 4.1 36.9 1.0
NE2 A:HIS626 4.2 37.5 1.0
O A:CYS618 4.2 23.0 1.0
O A:HIS626 4.3 32.4 1.0
N A:TRP620 4.4 17.8 1.0
C A:HIS626 4.4 31.9 1.0
CA A:TRP620 4.5 24.0 1.0
C A:CYS622 4.6 30.1 1.0
C A:CYS618 4.6 20.1 1.0
SD A:MET629 4.6 22.3 0.7
N A:HIS623 4.7 30.8 1.0
O A:PHE621 4.8 28.1 1.0
N A:HIS626 4.9 29.1 1.0
O A:HOH977 4.9 34.2 1.0
CB A:MET629 4.9 23.2 1.0
CA A:CYS618 5.0 19.2 1.0

Copper binding site 7 out of 12 in 7aq7

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Copper binding site 7 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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

b:37.4
occ:0.53
 CU1 B:CUZ708 0.0 37.4 0.5
NE2 B:HIS326 2.1 31.4 1.0
NE2 B:HIS382 2.3 38.5 1.0
S1 B:CUZ708 2.4 44.0 0.8
O B:HOH1143 2.9 40.2 1.0
NE2 B:HIS433 3.0 46.7 1.0
CD2 B:HIS326 3.0 29.6 1.0
CE1 B:HIS326 3.2 30.3 1.0
CD2 B:HIS433 3.2 42.4 1.0
CU3 B:CUZ708 3.3 25.0 0.5
CE1 B:HIS382 3.3 47.0 1.0
CD2 B:HIS382 3.3 44.9 1.0
CU4 B:CUZ708 3.3 42.9 0.7
CE1 B:HIS433 4.1 42.2 1.0
CG B:HIS326 4.2 31.4 1.0
ND1 B:HIS326 4.2 33.6 1.0
ND2 B:ASN241 4.3 27.1 1.0
CG B:HIS433 4.4 40.1 1.0
ND1 B:HIS382 4.4 42.8 1.0
CG B:HIS382 4.4 42.3 1.0
CU2 B:CUZ708 4.6 27.6 0.4
CE2 A:PHE621 4.6 27.9 1.0
ND1 B:HIS433 4.8 37.3 1.0

Copper binding site 8 out of 12 in 7aq7

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Copper binding site 8 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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

b:27.6
occ:0.39
 CU2 B:CUZ708 0.0 27.6 0.4
NE2 B:HIS178 2.2 26.5 1.0
S1 B:CUZ708 2.2 44.0 0.8
ND1 B:HIS129 2.6 31.8 1.0
CU3 B:CUZ708 2.7 25.0 0.5
CU4 B:CUZ708 2.8 42.9 0.7
CD2 B:HIS178 2.9 24.5 1.0
CG B:HIS129 3.2 26.1 1.0
CE1 B:HIS178 3.2 29.3 1.0
CB B:HIS129 3.4 21.8 1.0
CE1 B:HIS129 3.4 23.7 1.0
NE2 B:HIS130 3.4 22.9 1.0
O A:HOH1029 3.5 34.0 1.0
CE1 B:HIS130 3.6 25.1 1.0
ND1 B:HIS494 3.7 53.2 1.0
CG B:HIS178 4.1 23.0 1.0
CD2 B:HIS129 4.1 24.2 1.0
ND1 B:HIS178 4.2 28.7 1.0
NE2 B:HIS129 4.2 24.9 1.0
CG B:HIS494 4.3 44.8 1.0
CE1 B:HIS494 4.3 48.6 1.0
CD2 B:HIS130 4.5 24.7 1.0
CB B:HIS494 4.6 33.4 1.0
CU1 B:CUZ708 4.6 37.4 0.5
ND1 B:HIS130 4.7 20.8 1.0
NE2 B:HIS433 4.8 46.7 1.0
CA B:HIS129 4.8 21.8 1.0
OD1 B:ASN241 5.0 35.3 1.0

Copper binding site 9 out of 12 in 7aq7

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Copper binding site 9 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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

b:25.0
occ:0.48
 CU3 B:CUZ708 0.0 25.0 0.5
NE2 B:HIS130 2.2 22.9 1.0
NE2 B:HIS433 2.2 46.7 1.0
S1 B:CUZ708 2.2 44.0 0.8
CU2 B:CUZ708 2.7 27.6 0.4
CU4 B:CUZ708 2.9 42.9 0.7
CE1 B:HIS433 2.9 42.2 1.0
CD2 B:HIS130 3.0 24.7 1.0
CE1 B:HIS130 3.3 25.1 1.0
CU1 B:CUZ708 3.3 37.4 0.5
CD2 B:HIS433 3.3 42.4 1.0
OD1 B:ASN241 3.8 35.3 1.0
NE2 B:HIS178 4.0 26.5 1.0
ND1 B:HIS433 4.1 37.3 1.0
NE2 B:HIS382 4.1 38.5 1.0
CB B:HIS129 4.1 21.8 1.0
CG B:HIS130 4.2 23.1 1.0
CE1 B:HIS382 4.2 47.0 1.0
CB B:HIS494 4.3 33.4 1.0
CG B:HIS433 4.3 40.1 1.0
O B:HOH1076 4.3 49.4 1.0
ND1 B:HIS130 4.3 20.8 1.0
CE1 B:HIS178 4.3 29.3 1.0
O B:HOH1143 4.4 40.2 1.0
ND2 B:ASN241 4.5 27.1 1.0
CG B:ASN241 4.5 26.4 1.0
NE2 B:HIS326 4.6 31.4 1.0
ND1 B:HIS129 4.6 31.8 1.0
ND1 B:HIS494 4.8 53.2 1.0
CG B:HIS129 4.8 26.1 1.0
O B:HIS129 4.9 25.9 1.0
CG B:HIS494 4.9 44.8 1.0
CD2 B:HIS178 4.9 24.5 1.0

Copper binding site 10 out of 12 in 7aq7

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Copper binding site 10 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y


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

b:42.9
occ:0.67
 CU4 B:CUZ708 0.0 42.9 0.7
S1 B:CUZ708 2.3 44.0 0.8
O B:HOH1143 2.4 40.2 1.0
ND1 B:HIS494 2.4 53.2 1.0
CU2 B:CUZ708 2.8 27.6 0.4
CU3 B:CUZ708 2.9 25.0 0.5
CB B:HIS494 3.0 33.4 1.0
CG B:HIS494 3.0 44.8 1.0
CU1 B:CUZ708 3.3 37.4 0.5
CE1 B:HIS494 3.6 48.6 1.0
NE2 B:HIS433 3.6 46.7 1.0
CD2 B:HIS433 3.6 42.4 1.0
O A:HOH1029 3.7 34.0 1.0
ND1 B:HIS129 3.8 31.8 1.0
CA B:HIS494 4.1 29.1 1.0
CD2 B:HIS494 4.3 50.1 1.0
NZ B:LYS454 4.4 25.0 1.0
NE2 B:HIS494 4.5 46.5 1.0
CE2 A:PHE621 4.5 27.9 1.0
CD2 A:PHE621 4.6 29.2 1.0
CB B:HIS129 4.6 21.8 1.0
CG B:HIS129 4.7 26.1 1.0
NE2 B:HIS130 4.7 22.9 1.0
NE2 B:HIS178 4.7 26.5 1.0
O B:HOH975 4.7 27.2 1.0
CE1 B:HIS129 4.7 23.7 1.0
CE1 B:HIS433 4.8 42.2 1.0
C B:HIS494 4.8 24.5 1.0
CG B:HIS433 4.9 40.1 1.0
CE B:LYS454 4.9 27.3 1.0
NE2 B:HIS326 5.0 31.4 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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