Copper in PDB 6y7d: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A, PDB code: 6y7d was solved by L.Zhang, 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) 76.15 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.295, 76.152, 108.2, 90, 93.19, 90
R / Rfree (%) 16 / 20

Other elements in 6y7d:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A (pdb code 6y7d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A, PDB code: 6y7d:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6y7d

Go back to Copper Binding Sites List in 6y7d
Copper binding site 1 out of 4 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A


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, H433A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:40.7
occ:0.87
CU1 A:CUA708 0.0 40.7 0.9
SG A:CYS618 2.4 26.6 1.0
SD A:MET629 2.5 34.2 1.0
SG A:CYS622 2.5 30.6 0.8
CU2 A:CUA708 2.7 45.4 0.9
CB A:CYS618 3.1 19.2 1.0
CB A:CYS622 3.4 31.3 1.0
CE A:MET629 3.4 32.1 1.0
CD2 A:HIS583 3.5 37.0 1.0
CG A:MET629 3.7 29.5 1.0
O A:TRP620 4.0 25.1 1.0
CG A:HIS583 4.0 27.8 1.0
CB A:MET629 4.1 27.6 1.0
CB A:HIS583 4.2 22.0 1.0
CA A:HIS583 4.4 23.2 1.0
NE2 A:HIS583 4.4 36.1 1.0
CA A:CYS618 4.6 17.9 1.0
CA A:CYS622 4.7 41.1 1.0
O A:SER582 4.7 22.6 1.0
ND1 A:HIS626 4.8 36.9 1.0
N A:CYS622 4.8 32.2 1.0
CB A:ALA552 4.9 36.1 1.0
N A:GLY584 4.9 26.0 1.0
CA A:ALA552 5.0 35.4 1.0

Copper binding site 2 out of 4 in 6y7d

Go back to Copper Binding Sites List in 6y7d
Copper binding site 2 out of 4 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A


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, H433A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:45.4
occ:0.86
CU2 A:CUA708 0.0 45.4 0.9
ND1 A:HIS626 2.2 36.9 1.0
O A:TRP620 2.5 25.1 1.0
CU1 A:CUA708 2.7 40.7 0.9
SG A:CYS622 2.7 30.6 0.8
SG A:CYS618 2.8 26.6 1.0
CG A:HIS626 3.1 39.4 1.0
N A:CYS622 3.2 32.2 1.0
CE1 A:HIS626 3.2 39.4 1.0
CB A:HIS626 3.3 31.2 1.0
C A:TRP620 3.4 28.7 1.0
CB A:CYS622 3.4 31.3 1.0
CB A:CYS618 3.7 19.2 1.0
CA A:PHE621 3.8 37.7 1.0
CA A:HIS626 3.9 40.7 1.0
C A:PHE621 3.9 34.5 1.0
CA A:CYS622 3.9 41.1 1.0
N A:PHE621 3.9 36.3 1.0
O A:CYS618 4.0 22.4 1.0
CD2 A:HIS626 4.3 42.7 1.0
O A:HIS626 4.3 40.2 1.0
NE2 A:HIS626 4.3 41.9 1.0
C A:CYS618 4.4 20.4 1.0
C A:HIS626 4.4 43.4 1.0
N A:TRP620 4.4 25.5 1.0
CA A:TRP620 4.5 27.6 1.0
CA A:CYS618 4.7 17.9 1.0
SD A:MET629 4.8 34.2 1.0
CB A:MET629 4.8 27.6 1.0
C A:CYS622 4.9 40.1 1.0
O A:HOH1027 4.9 31.4 1.0
O A:PHE621 4.9 32.1 1.0
C A:SER619 4.9 25.7 1.0
N A:HIS623 5.0 33.5 1.0

Copper binding site 3 out of 4 in 6y7d

Go back to Copper Binding Sites List in 6y7d
Copper binding site 3 out of 4 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A


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, H433A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu907

b:37.8
occ:0.82
CU1 B:CUA907 0.0 37.8 0.8
SD B:MET629 2.4 24.0 0.9
SG B:CYS618 2.5 24.3 1.0
SG B:CYS622 2.6 28.4 0.8
CU2 B:CUA907 2.7 47.2 0.9
CE B:MET629 3.2 23.4 1.0
CB B:CYS618 3.2 17.6 1.0
CB B:CYS622 3.4 31.8 1.0
CG B:MET629 3.6 26.0 1.0
CD2 B:HIS583 3.9 30.8 1.0
CB B:MET629 4.0 18.7 1.0
O B:TRP620 4.1 30.4 1.0
CG B:HIS583 4.1 24.9 1.0
CB B:HIS583 4.1 22.6 1.0
CA B:HIS583 4.2 20.6 1.0
CA B:CYS618 4.7 15.0 1.0
O B:SER582 4.7 20.3 1.0
ND1 B:HIS626 4.7 41.8 1.0
NE2 B:HIS583 4.7 28.5 1.0
CA B:CYS622 4.8 38.3 1.0
N B:GLY584 4.8 19.3 1.0
CB B:ALA552 4.9 33.0 1.0
N B:CYS622 5.0 34.7 1.0
CA B:ALA552 5.0 34.5 1.0

Copper binding site 4 out of 4 in 6y7d

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Copper binding site 4 out of 4 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H433A


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, H433A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu907

b:47.2
occ:0.90
CU2 B:CUA907 0.0 47.2 0.9
ND1 B:HIS626 2.1 41.8 1.0
O B:TRP620 2.5 30.4 1.0
CU1 B:CUA907 2.7 37.8 0.8
SG B:CYS622 2.7 28.4 0.8
SG B:CYS618 2.8 24.3 1.0
CG B:HIS626 3.0 38.0 1.0
CE1 B:HIS626 3.1 36.5 1.0
CB B:HIS626 3.3 32.8 1.0
N B:CYS622 3.5 34.7 1.0
CB B:CYS622 3.5 31.8 1.0
C B:TRP620 3.5 39.1 1.0
CB B:CYS618 3.6 17.6 1.0
CA B:HIS626 3.8 38.7 1.0
CA B:PHE621 4.0 43.2 1.0
O B:HIS626 4.0 32.2 1.0
O B:CYS618 4.1 20.8 1.0
C B:PHE621 4.1 37.2 1.0
CA B:CYS622 4.1 38.3 1.0
N B:PHE621 4.2 40.4 1.0
CD2 B:HIS626 4.2 42.5 1.0
NE2 B:HIS626 4.2 44.4 1.0
C B:HIS626 4.3 36.0 1.0
C B:CYS618 4.4 18.9 1.0
N B:TRP620 4.5 25.2 1.0
O B:HOH1140 4.6 28.2 1.0
SD B:MET629 4.6 24.0 0.9
CA B:TRP620 4.7 27.6 1.0
CA B:CYS618 4.7 15.0 1.0
CB B:MET629 4.7 18.7 1.0
C B:CYS622 4.9 42.6 1.0
N B:HIS623 5.0 45.2 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 Mar 3 13:07:56 2021

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