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: Mon Jul 14 07:47:15 2025

Last articles

Mg in 2X0Q
Mg in 2X03
Mg in 2WZG
Mg in 2WZD
Mg in 2WZC
Mg in 2WZB
Mg in 2WZ8
Mg in 2WX5
Mg in 2WWR
Mg in 2WW8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy