Atomistry » Copper » PDB 7a8v-7ev7 » 7aq3
Atomistry »
  Copper »
    PDB 7a8v-7ev7 »
      7aq3 »

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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Go back to Copper Binding Sites List in 7aq3
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy