Atomistry » Copper » PDB 7a8v-7ev7 » 7apy
Atomistry »
  Copper »
    PDB 7a8v-7ev7 »
      7apy »

Copper in PDB 7apy: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A

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

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A, PDB code: 7apy 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) 68.84 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.964, 76.627, 108.563, 90, 93.41, 90
R / Rfree (%) 16.6 / 22.5

Other elements in 7apy:

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

Sodium (Na) 2 atoms
Chlorine (Cl) 3 atoms
Calcium (Ca) 2 atoms
Potassium (K) 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, D576A (pdb code 7apy). 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, D576A, PDB code: 7apy:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 1 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:57.4
occ:0.51
 CU1 A:CUZ713 0.0 57.4 0.5
NE2 A:HIS326 2.2 30.7 1.0
NE2 A:HIS382 2.4 27.6 0.6
S1 A:CUZ713 2.5 65.2 1.0
NE2 A:HIS433 2.9 45.0 1.0
CD2 A:HIS433 2.9 43.9 1.0
CE1 A:HIS326 3.1 35.3 1.0
CD2 A:HIS326 3.2 32.6 1.0
CD2 A:HIS382 3.3 27.0 0.6
CU3 A:CUZ713 3.3 26.7 0.6
CU4 A:CUZ713 3.4 33.8 0.6
O A:HOH1150 3.4 41.9 1.0
CE1 A:HIS382 3.5 27.7 0.6
CE1 A:HIS433 4.2 40.3 1.0
CG A:HIS433 4.2 36.6 1.0
ND1 A:HIS326 4.3 29.9 1.0
CG A:HIS326 4.3 26.8 1.0
CG A:HIS382 4.5 27.0 0.6
ND1 A:HIS382 4.5 24.9 0.6
CU2 A:CUZ713 4.6 41.4 0.2
CE2 B:PHE621 4.6 37.1 1.0
ND1 A:HIS433 4.8 40.8 1.0
ND2 A:ASN241 4.8 36.9 1.0
N A:HIS433 4.9 18.3 1.0
C A:GLY432 4.9 28.8 1.0

Copper binding site 2 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 2 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:41.4
occ:0.25
 CU2 A:CUZ713 0.0 41.4 0.2
S1 A:CUZ713 2.2 65.2 1.0
NE2 A:HIS178 2.2 29.9 1.0
CD2 A:HIS129 2.5 25.1 1.0
CU3 A:CUZ713 2.7 26.7 0.6
CU4 A:CUZ713 2.8 33.8 0.6
O A:HOH1209 3.0 35.2 1.0
CG A:HIS129 3.0 20.2 1.0
CD2 A:HIS178 3.1 29.9 1.0
CE1 A:HIS178 3.2 32.7 1.0
NE2 A:HIS130 3.3 19.1 1.0
CB A:HIS129 3.4 11.5 1.0
NE2 A:HIS129 3.5 24.8 1.0
CE1 A:HIS130 3.7 18.4 1.0
ND1 A:HIS129 4.1 26.3 1.0
CD2 A:HIS494 4.1 77.6 1.0
CG A:HIS178 4.2 33.1 1.0
ND1 A:HIS178 4.2 35.5 1.0
CE1 A:HIS129 4.3 22.5 1.0
CD2 A:HIS130 4.4 14.0 1.0
CG A:HIS494 4.5 64.3 1.0
CU1 A:CUZ713 4.6 57.4 0.5
CB A:HIS494 4.6 35.1 1.0
CA A:HIS129 4.7 20.1 1.0
SD B:MET627 4.8 44.3 0.7
ND1 A:HIS130 4.8 20.6 1.0
NE2 A:HIS494 4.8 79.5 1.0
NE2 A:HIS433 4.8 45.0 1.0

Copper binding site 3 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 3 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:26.7
occ:0.55
 CU3 A:CUZ713 0.0 26.7 0.6
S1 A:CUZ713 2.2 65.2 1.0
NE2 A:HIS433 2.2 45.0 1.0
NE2 A:HIS130 2.3 19.1 1.0
CU2 A:CUZ713 2.7 41.4 0.2
CU4 A:CUZ713 2.8 33.8 0.6
CE1 A:HIS433 2.9 40.3 1.0
CD2 A:HIS130 3.1 14.0 1.0
CD2 A:HIS433 3.3 43.9 1.0
CU1 A:CUZ713 3.3 57.4 0.5
CE1 A:HIS130 3.4 18.4 1.0
OD1 A:ASN241 3.8 38.0 1.0
ND1 A:HIS433 4.0 40.8 1.0
NE2 A:HIS382 4.2 27.6 0.6
NE2 A:HIS178 4.2 29.9 1.0
CG A:HIS433 4.2 36.6 1.0
CB A:HIS129 4.2 11.5 1.0
CG A:HIS130 4.3 20.3 1.0
O A:HOH1174 4.3 35.3 1.0
CE1 A:HIS382 4.3 27.7 0.6
CE1 A:HIS178 4.4 32.7 1.0
ND1 A:HIS130 4.4 20.6 1.0
CB A:HIS494 4.5 35.1 1.0
NE2 A:HIS326 4.5 30.7 1.0
O A:HOH1150 4.6 41.9 1.0
CD2 A:HIS129 4.7 25.1 1.0
CG A:ASN241 4.7 25.3 1.0
CE1 A:HIS326 4.8 35.3 1.0
CG A:HIS129 4.8 20.2 1.0
ND2 A:ASN241 4.9 36.9 1.0
O A:HIS129 5.0 22.6 1.0

Copper binding site 4 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 4 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:33.8
occ:0.59
 CU4 A:CUZ713 0.0 33.8 0.6
S1 A:CUZ713 2.4 65.2 1.0
O A:HOH1150 2.4 41.9 1.0
CD2 A:HIS494 2.8 77.6 1.0
CU2 A:CUZ713 2.8 41.4 0.2
CU3 A:CUZ713 2.8 26.7 0.6
CB A:HIS494 2.8 35.1 1.0
CG A:HIS494 3.0 64.3 1.0
CU1 A:CUZ713 3.4 57.4 0.5
O A:HOH1209 3.7 35.2 1.0
CD2 A:HIS129 3.7 25.1 1.0
CD2 A:HIS433 3.7 43.9 1.0
NE2 A:HIS433 3.8 45.0 1.0
NE2 A:HIS494 4.1 79.5 1.0
CA A:HIS494 4.1 35.7 1.0
ND1 A:HIS494 4.3 78.3 1.0
NZ A:LYS454 4.4 28.5 1.0
CG A:HIS129 4.5 20.2 1.0
CB A:HIS129 4.6 11.5 1.0
NE2 A:HIS130 4.6 19.1 1.0
C A:HIS494 4.6 21.5 1.0
CE2 B:PHE621 4.7 37.1 1.0
CE1 A:HIS494 4.8 75.7 1.0
CE1 A:HIS433 4.8 40.3 1.0
CD2 B:PHE621 4.8 38.6 1.0
NE2 A:HIS129 4.8 24.8 1.0
O A:HOH1021 4.8 20.1 1.0
CG A:HIS433 4.8 36.6 1.0
O A:HIS494 4.9 25.6 1.0
NE2 A:HIS178 4.9 29.9 1.0
O A:HOH1035 4.9 65.9 1.0

Copper binding site 5 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 5 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu714

b:34.8
occ:0.91
 CU1 A:CUA714 0.0 34.8 0.9
SG A:CYS618 2.4 20.8 0.9
SD A:MET629 2.4 23.1 1.0
SG A:CYS622 2.6 23.7 0.8
CU2 A:CUA714 2.7 34.3 0.9
CD2 A:HIS583 3.2 33.3 1.0
CE A:MET629 3.2 27.2 1.0
CB A:CYS618 3.2 13.4 1.0
CB A:CYS622 3.4 23.4 1.0
CG A:HIS583 3.7 26.8 1.0
CG A:MET629 3.8 21.5 1.0
CB A:HIS583 3.9 13.7 1.0
O A:TRP620 4.0 18.4 1.0
NE2 A:HIS583 4.1 35.8 1.0
CA A:HIS583 4.2 16.4 1.0
CB A:MET629 4.3 19.5 1.0
CA A:CYS618 4.6 13.5 1.0
O A:SER582 4.7 19.0 1.0
ND1 A:HIS583 4.7 33.4 1.0
ND1 A:HIS626 4.7 27.7 1.0
CA A:CYS622 4.8 28.6 1.0
N A:GLY584 4.8 18.8 1.0
CE1 A:HIS583 4.9 30.6 1.0
N A:CYS622 4.9 26.6 1.0
CA A:ALA552 5.0 23.4 1.0
CB A:ALA552 5.0 29.1 1.0

Copper binding site 6 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 6 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu714

b:34.3
occ:0.89
 CU2 A:CUA714 0.0 34.3 0.9
ND1 A:HIS626 2.1 27.7 1.0
O A:TRP620 2.5 18.4 1.0
SG A:CYS622 2.6 23.7 0.8
CU1 A:CUA714 2.7 34.8 0.9
SG A:CYS618 2.7 20.8 0.9
CG A:HIS626 3.1 27.8 1.0
CE1 A:HIS626 3.1 27.9 1.0
N A:CYS622 3.3 26.6 1.0
CB A:HIS626 3.4 28.3 1.0
CB A:CYS622 3.4 23.4 1.0
C A:TRP620 3.5 19.6 1.0
CB A:CYS618 3.6 13.4 1.0
CA A:HIS626 3.9 25.8 1.0
CA A:PHE621 3.9 28.8 1.0
CA A:CYS622 3.9 28.6 1.0
C A:PHE621 4.0 27.9 1.0
N A:PHE621 4.1 25.7 1.0
O A:HIS626 4.1 22.5 1.0
O A:CYS618 4.2 21.7 1.0
NE2 A:HIS626 4.2 31.9 1.0
CD2 A:HIS626 4.2 32.8 1.0
N A:TRP620 4.4 23.4 1.0
SD A:MET629 4.4 23.1 1.0
C A:CYS618 4.4 16.0 1.0
C A:HIS626 4.5 30.8 1.0
CA A:TRP620 4.5 25.3 1.0
CA A:CYS618 4.6 13.5 1.0
O A:HOH827 4.7 26.1 1.0
CB A:MET629 4.7 19.5 1.0
C A:CYS622 4.8 30.7 1.0
N A:HIS623 5.0 31.6 1.0

Copper binding site 7 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 7 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:43.6
occ:0.41
 CU1 B:CUZ709 0.0 43.6 0.4
NE2 B:HIS326 2.2 34.8 1.0
NE2 B:HIS382 2.4 25.6 0.5
S1 B:CUZ709 2.4 59.6 1.0
NE2 B:HIS433 2.6 47.7 1.0
CD2 B:HIS433 2.7 46.8 1.0
CD2 B:HIS382 3.0 25.3 0.5
CD2 B:HIS326 3.0 34.1 1.0
CU3 B:CUZ709 3.3 28.0 0.5
CE1 B:HIS326 3.3 30.8 1.0
CU4 B:CUZ709 3.3 38.9 0.6
CE1 B:HIS382 3.5 26.5 0.5
CE1 B:HIS433 3.9 38.9 1.0
O B:HOH1007 4.0 44.1 1.0
CG B:HIS433 4.0 35.1 1.0
CG B:HIS382 4.2 23.7 0.5
CG B:HIS326 4.2 35.8 1.0
ND1 B:HIS326 4.3 34.9 1.0
ND2 B:ASN241 4.4 38.0 1.0
ND1 B:HIS382 4.5 27.6 0.5
ND1 B:HIS433 4.5 37.3 1.0
CU2 B:CUZ709 4.6 35.9 0.4
N B:HIS433 4.8 23.6 1.0
C B:GLY432 4.9 28.8 1.0
CE2 A:PHE621 4.9 27.3 1.0
OD1 B:ASN241 5.0 40.5 1.0

Copper binding site 8 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 8 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, 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, D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:35.9
occ:0.42
 CU2 B:CUZ709 0.0 35.9 0.4
NE2 B:HIS178 2.2 32.8 1.0
S1 B:CUZ709 2.2 59.6 1.0
ND1 B:HIS129 2.6 36.3 1.0
CU3 B:CUZ709 2.7 28.0 0.5
CU4 B:CUZ709 2.8 38.9 0.6
CE1 B:HIS178 3.0 27.9 1.0
CD2 B:HIS178 3.1 25.8 1.0
CG B:HIS129 3.4 23.5 1.0
O A:HOH1115 3.4 35.9 1.0
CE1 B:HIS129 3.4 29.8 1.0
NE2 B:HIS130 3.4 22.3 1.0
CB B:HIS129 3.6 20.1 1.0
CE1 B:HIS130 3.7 23.8 1.0
ND1 B:HIS494 3.8 59.1 1.0
ND1 B:HIS178 4.1 31.9 1.0
CG B:HIS178 4.2 29.7 1.0
CD2 B:HIS129 4.4 27.5 1.0
NE2 B:HIS129 4.4 31.2 1.0
CE1 B:HIS494 4.4 56.1 1.0
CG B:HIS494 4.5 53.4 1.0
CD2 B:HIS130 4.5 19.7 1.0
CU1 B:CUZ709 4.6 43.6 0.4
CB B:HIS494 4.7 35.3 1.0
NE2 B:HIS433 4.8 47.7 1.0
ND1 B:HIS130 4.9 21.5 1.0
SD A:MET627 4.9 23.3 0.5

Copper binding site 9 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 9 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A


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

b:28.0
occ:0.47
 CU3 B:CUZ709 0.0 28.0 0.5
NE2 B:HIS130 2.2 22.3 1.0
S1 B:CUZ709 2.2 59.6 1.0
NE2 B:HIS433 2.3 47.7 1.0
CU2 B:CUZ709 2.7 35.9 0.4
CE1 B:HIS433 2.8 38.9 1.0
CU4 B:CUZ709 2.9 38.9 0.6
CD2 B:HIS130 2.9 19.7 1.0
CE1 B:HIS130 3.3 23.8 1.0
CU1 B:CUZ709 3.3 43.6 0.4
CD2 B:HIS433 3.4 46.8 1.0
OD1 B:ASN241 3.7 40.5 1.0
ND1 B:HIS433 4.0 37.3 1.0
CB B:HIS129 4.1 20.1 1.0
CG B:HIS130 4.2 24.2 1.0
CG B:HIS433 4.2 35.1 1.0
NE2 B:HIS178 4.2 32.8 1.0
NE2 B:HIS382 4.2 25.6 0.5
CB B:HIS494 4.3 35.3 1.0
ND1 B:HIS130 4.3 21.5 1.0
O B:HOH1064 4.3 51.9 1.0
CE1 B:HIS178 4.4 27.9 1.0
CE1 B:HIS382 4.5 26.5 0.5
NE2 B:HIS326 4.5 34.8 1.0
ND1 B:HIS129 4.5 36.3 1.0
O B:HOH1007 4.6 44.1 1.0
CG B:ASN241 4.6 30.9 1.0
ND2 B:ASN241 4.7 38.0 1.0
CG B:HIS129 4.8 23.5 1.0
ND1 B:HIS494 4.8 59.1 1.0
O B:HIS129 4.9 26.4 1.0
CG B:HIS494 4.9 53.4 1.0

Copper binding site 10 out of 12 in 7apy

Go back to Copper Binding Sites List in 7apy
Copper binding site 10 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A


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

b:38.9
occ:0.55
 CU4 B:CUZ709 0.0 38.9 0.6
O B:HOH1007 2.3 44.1 1.0
S1 B:CUZ709 2.3 59.6 1.0
ND1 B:HIS494 2.5 59.1 1.0
CU2 B:CUZ709 2.8 35.9 0.4
CU3 B:CUZ709 2.9 28.0 0.5
CB B:HIS494 3.1 35.3 1.0
CG B:HIS494 3.2 53.4 1.0
CU1 B:CUZ709 3.3 43.6 0.4
O A:HOH1115 3.6 35.9 1.0
CE1 B:HIS494 3.7 56.1 1.0
NE2 B:HIS433 3.8 47.7 1.0
CD2 B:HIS433 3.8 46.8 1.0
ND1 B:HIS129 3.8 36.3 1.0
CA B:HIS494 4.2 31.4 1.0
CD2 B:HIS494 4.4 54.9 1.0
NZ B:LYS454 4.5 29.6 1.0
CE2 A:PHE621 4.5 27.3 1.0
CD2 A:PHE621 4.6 32.4 1.0
NE2 B:HIS494 4.7 55.9 1.0
CB B:HIS129 4.7 20.1 1.0
CG B:HIS129 4.7 23.5 1.0
CE1 B:HIS129 4.7 29.8 1.0
NE2 B:HIS130 4.7 22.3 1.0
CE1 B:HIS433 4.8 38.9 1.0
NE2 B:HIS178 4.9 32.8 1.0
C B:HIS494 4.9 27.5 1.0
O B:HOH853 4.9 23.2 1.0
CG B:HIS433 4.9 35.1 1.0
NE2 B:HIS326 4.9 34.8 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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy