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Copper in PDB 6rkz: Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II

Enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II

All present enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II:
1.7.2.4;

Protein crystallography data

The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II, PDB code: 6rkz was solved by L.Zhang, A.Wuest, B.Prasser, C.Mueller, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.70 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.887, 76.789, 108.823, 90.00, 93.33, 90.00
R / Rfree (%) 15.2 / 19.1

Other elements in 6rkz:

The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II also contains other interesting chemical elements:

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

Copper Binding Sites:

Pages:

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

Binding sites:

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

Copper binding site 1 out of 12 in 6rkz

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Copper binding site 1 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:36.0
occ:0.63
 CU1 A:CUZ713 0.0 36.0 0.6
NE2 A:HIS326 2.2 25.3 1.0
NE2 A:HIS382 2.2 33.6 1.0
S1 A:CUZ713 2.4 35.0 0.9
CE1 A:HIS326 3.1 32.9 1.0
CU3 A:CUZ713 3.2 24.6 0.7
CD2 A:HIS326 3.2 24.2 1.0
CD2 A:HIS382 3.2 32.9 1.0
CE1 A:HIS382 3.2 34.8 1.0
NE2 A:HIS433 3.3 28.9 1.0
CU4 A:CUZ713 3.4 30.3 0.7
O A:HOH1173 3.4 33.4 1.0
CD2 A:HIS433 3.6 35.6 1.0
CE1 A:HIS433 4.0 31.6 1.0
ND1 A:HIS326 4.2 25.6 1.0
CG A:HIS326 4.3 23.7 1.0
ND1 A:HIS382 4.3 28.4 1.0
CG A:HIS382 4.4 29.0 1.0
CG A:HIS433 4.4 34.2 1.0
ND2 A:ASN241 4.5 26.0 1.0
CU2 A:CUZ713 4.6 15.5 0.3
ND1 A:HIS433 4.6 27.9 1.0
CE2 B:PHE621 4.9 34.0 1.0
N A:HIS433 5.0 23.4 1.0

Copper binding site 2 out of 12 in 6rkz

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Copper binding site 2 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:15.5
occ:0.31
 CU2 A:CUZ713 0.0 15.5 0.3
NE2 A:HIS178 2.2 31.2 1.0
S1 A:CUZ713 2.2 35.0 0.9
ND1 A:HIS129 2.3 32.1 1.0
CU3 A:CUZ713 2.7 24.6 0.7
CU4 A:CUZ713 2.8 30.3 0.7
CD2 A:HIS178 2.9 30.4 1.0
CG A:HIS129 3.1 28.7 1.0
NE2 A:HIS130 3.2 22.5 1.0
CE1 A:HIS178 3.2 33.3 1.0
CE1 A:HIS129 3.3 34.5 1.0
CB A:HIS129 3.3 21.4 1.0
O B:HOH1099 3.4 32.6 1.0
CE1 A:HIS130 3.4 18.3 1.0
ND1 A:HIS494 3.8 47.9 1.0
CG A:HIS178 4.0 30.6 1.0
ND1 A:HIS178 4.2 32.7 1.0
CD2 A:HIS129 4.2 29.2 1.0
CD2 A:HIS130 4.2 18.0 1.0
NE2 A:HIS129 4.3 27.5 1.0
CG A:HIS494 4.4 39.8 1.0
CE1 A:HIS494 4.4 45.0 1.0
ND1 A:HIS130 4.5 19.8 1.0
CU1 A:CUZ713 4.6 36.0 0.6
CB A:HIS494 4.6 37.8 1.0
NE2 A:HIS433 4.8 28.9 1.0
CA A:HIS129 4.8 22.5 1.0
SD B:MET627 4.9 27.4 0.7
CG A:HIS130 5.0 19.1 1.0
OD1 A:ASN241 5.0 28.5 1.0

Copper binding site 3 out of 12 in 6rkz

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Copper binding site 3 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:24.6
occ:0.66
 CU3 A:CUZ713 0.0 24.6 0.7
NE2 A:HIS130 2.1 22.5 1.0
NE2 A:HIS433 2.2 28.9 1.0
S1 A:CUZ713 2.2 35.0 0.9
CU2 A:CUZ713 2.7 15.5 0.3
CU4 A:CUZ713 2.8 30.3 0.7
CD2 A:HIS130 2.8 18.0 1.0
CE1 A:HIS433 3.1 31.6 1.0
CU1 A:CUZ713 3.2 36.0 0.6
CD2 A:HIS433 3.2 35.6 1.0
CE1 A:HIS130 3.2 18.3 1.0
OD1 A:ASN241 3.9 28.5 1.0
CG A:HIS130 4.1 19.1 1.0
NE2 A:HIS382 4.1 33.6 1.0
NE2 A:HIS178 4.1 31.2 1.0
CB A:HIS129 4.1 21.4 1.0
O A:HOH1050 4.2 31.1 1.0
CB A:HIS494 4.2 37.8 1.0
ND1 A:HIS130 4.2 19.8 1.0
ND1 A:HIS433 4.2 27.9 1.0
CG A:HIS433 4.3 34.2 1.0
CE1 A:HIS382 4.3 34.8 1.0
O A:HOH1173 4.4 33.4 1.0
CE1 A:HIS178 4.4 33.3 1.0
ND1 A:HIS129 4.5 32.1 1.0
O A:HIS129 4.7 24.0 1.0
ND1 A:HIS494 4.7 47.9 1.0
CG A:ASN241 4.8 24.4 1.0
NE2 A:HIS326 4.8 25.3 1.0
CG A:HIS129 4.8 28.7 1.0
CG A:HIS494 4.8 39.8 1.0
ND2 A:ASN241 4.9 26.0 1.0

Copper binding site 4 out of 12 in 6rkz

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Copper binding site 4 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu713

b:30.3
occ:0.71
 CU4 A:CUZ713 0.0 30.3 0.7
O A:HOH1173 2.3 33.4 1.0
S1 A:CUZ713 2.3 35.0 0.9
ND1 A:HIS494 2.4 47.9 1.0
CU2 A:CUZ713 2.8 15.5 0.3
CU3 A:CUZ713 2.8 24.6 0.7
CB A:HIS494 3.0 37.8 1.0
CG A:HIS494 3.1 39.8 1.0
CU1 A:CUZ713 3.4 36.0 0.6
CE1 A:HIS494 3.5 45.0 1.0
O B:HOH1099 3.6 32.6 1.0
NE2 A:HIS433 3.7 28.9 1.0
ND1 A:HIS129 3.7 32.1 1.0
CD2 A:HIS433 3.7 35.6 1.0
CA A:HIS494 4.2 33.4 1.0
CD2 A:HIS494 4.3 44.6 1.0
NZ A:LYS454 4.4 31.0 1.0
NE2 A:HIS130 4.5 22.5 1.0
NE2 A:HIS494 4.5 38.5 1.0
CB A:HIS129 4.5 21.4 1.0
CG A:HIS129 4.6 28.7 1.0
CE1 A:HIS129 4.6 34.5 1.0
CE2 B:PHE621 4.7 34.0 1.0
NE2 A:HIS178 4.7 31.2 1.0
CD2 B:PHE621 4.8 32.0 1.0
C A:HIS494 4.9 20.6 1.0
CE A:LYS454 5.0 31.7 1.0
O A:HOH1090 5.0 28.6 1.0
CE1 A:HIS433 5.0 31.6 1.0

Copper binding site 5 out of 12 in 6rkz

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Copper binding site 5 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu714

b:33.9
occ:1.00
 CU1 A:CUA714 0.0 33.9 1.0
SG A:CYS618 2.3 19.4 0.8
SD A:MET629 2.4 25.7 1.0
SG A:CYS622 2.4 26.2 1.0
CU2 A:CUA714 2.6 37.2 1.0
CB A:CYS618 3.2 19.1 1.0
CE A:MET629 3.3 23.6 1.0
CB A:CYS622 3.5 22.5 1.0
CD2 A:HIS583 3.6 36.0 1.0
CG A:MET629 3.7 24.5 1.0
O A:TRP620 3.9 21.6 1.0
CG A:HIS583 4.0 24.7 1.0
CB A:HIS583 4.1 25.6 1.0
CB A:MET629 4.2 28.3 1.0
CA A:HIS583 4.3 22.0 1.0
ND1 A:HIS626 4.5 27.4 1.0
NE2 A:HIS583 4.5 27.1 1.0
CA A:CYS618 4.6 19.0 1.0
O A:SER582 4.8 22.0 1.0
CA A:CYS622 4.8 28.2 1.0
N A:GLY584 4.8 19.0 1.0
N A:CYS622 4.9 26.3 1.0

Copper binding site 6 out of 12 in 6rkz

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Copper binding site 6 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu714

b:37.2
occ:1.00
 CU2 A:CUA714 0.0 37.2 1.0
ND1 A:HIS626 2.0 27.4 1.0
SG A:CYS622 2.5 26.2 1.0
O A:TRP620 2.5 21.6 1.0
CU1 A:CUA714 2.6 33.9 1.0
SG A:CYS618 2.8 19.4 0.8
CE1 A:HIS626 2.9 30.2 1.0
CG A:HIS626 3.1 25.2 1.0
N A:CYS622 3.2 26.3 1.0
CB A:CYS622 3.4 22.5 1.0
C A:TRP620 3.5 19.3 1.0
CB A:HIS626 3.6 30.6 1.0
CB A:CYS618 3.7 19.1 1.0
CA A:HIS626 3.8 31.3 1.0
CA A:PHE621 3.9 28.6 1.0
CA A:CYS622 3.9 28.2 1.0
C A:PHE621 3.9 29.2 1.0
NE2 A:HIS626 4.0 27.6 1.0
N A:PHE621 4.1 25.1 1.0
CD2 A:HIS626 4.2 28.4 1.0
O A:CYS618 4.2 23.5 1.0
O A:HIS626 4.2 28.0 1.0
SD A:MET629 4.4 25.7 1.0
N A:TRP620 4.5 23.7 1.0
C A:HIS626 4.5 30.4 1.0
CA A:TRP620 4.5 20.5 1.0
C A:CYS618 4.6 21.0 1.0
CB A:MET629 4.7 28.3 1.0
C A:CYS622 4.7 26.5 1.0
CA A:CYS618 4.8 19.0 1.0
N A:HIS623 4.8 28.1 1.0
O A:HOH956 4.9 25.6 1.0
O A:PHE621 5.0 23.7 1.0

Copper binding site 7 out of 12 in 6rkz

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Copper binding site 7 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:35.3
occ:0.70
 CU1 B:CUZ709 0.0 35.3 0.7
NE2 B:HIS382 2.2 33.2 1.0
NE2 B:HIS326 2.2 29.3 1.0
S1 B:CUZ709 2.4 33.9 0.9
CU3 B:CUZ709 3.1 25.3 0.6
CD2 B:HIS326 3.1 31.1 1.0
CE1 B:HIS382 3.1 39.3 1.0
O B:HOH1122 3.2 35.8 1.0
CD2 B:HIS382 3.2 33.8 1.0
CU4 B:CUZ709 3.3 32.2 0.7
NE2 B:HIS433 3.3 33.5 1.0
CE1 B:HIS326 3.3 31.6 1.0
CD2 B:HIS433 3.5 34.8 1.0
CE1 B:HIS433 4.1 32.7 1.0
ND2 B:ASN241 4.3 34.7 1.0
ND1 B:HIS382 4.3 35.5 1.0
CG B:HIS326 4.3 30.9 1.0
ND1 B:HIS326 4.3 33.2 1.0
CG B:HIS382 4.4 35.3 1.0
CG B:HIS433 4.4 32.6 1.0
CU2 B:CUZ709 4.5 25.4 0.5
ND1 B:HIS433 4.7 27.1 1.0
CE2 A:PHE621 4.9 25.6 1.0
OD1 B:ASN241 4.9 31.4 1.0

Copper binding site 8 out of 12 in 6rkz

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Copper binding site 8 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:25.4
occ:0.51
 CU2 B:CUZ709 0.0 25.4 0.5
NE2 B:HIS178 2.2 28.1 1.0
S1 B:CUZ709 2.2 33.9 0.9
ND1 B:HIS129 2.2 33.6 1.0
CU3 B:CUZ709 2.8 25.3 0.6
CU4 B:CUZ709 2.8 32.2 0.7
CD2 B:HIS178 2.9 25.5 1.0
CE1 B:HIS129 3.2 29.9 1.0
CG B:HIS129 3.2 26.8 1.0
CE1 B:HIS178 3.2 27.3 1.0
NE2 B:HIS130 3.4 24.3 1.0
O A:HOH1192 3.4 32.8 1.0
ND1 B:HIS494 3.5 32.2 1.0
CB B:HIS129 3.5 23.1 1.0
CE1 B:HIS130 3.6 26.5 1.0
CE1 B:HIS494 4.1 30.8 1.0
CG B:HIS178 4.1 23.6 1.0
ND1 B:HIS178 4.2 28.1 1.0
NE2 B:HIS129 4.2 28.1 1.0
CD2 B:HIS129 4.3 23.3 1.0
CG B:HIS494 4.3 31.4 1.0
CD2 B:HIS130 4.5 23.1 1.0
CU1 B:CUZ709 4.5 35.3 0.7
CB B:HIS494 4.7 27.7 1.0
ND1 B:HIS130 4.7 25.5 1.0
NE2 B:HIS433 4.8 33.5 1.0
CA B:HIS129 5.0 24.1 1.0
OD1 B:ASN241 5.0 31.4 1.0

Copper binding site 9 out of 12 in 6rkz

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Copper binding site 9 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:25.3
occ:0.61
 CU3 B:CUZ709 0.0 25.3 0.6
NE2 B:HIS130 2.1 24.3 1.0
NE2 B:HIS433 2.2 33.5 1.0
S1 B:CUZ709 2.2 33.9 0.9
CU2 B:CUZ709 2.8 25.4 0.5
CU4 B:CUZ709 2.8 32.2 0.7
CD2 B:HIS130 3.0 23.1 1.0
CU1 B:CUZ709 3.1 35.3 0.7
CE1 B:HIS433 3.1 32.7 1.0
CD2 B:HIS433 3.2 34.8 1.0
CE1 B:HIS130 3.2 26.5 1.0
OD1 B:ASN241 3.8 31.4 1.0
NE2 B:HIS382 4.0 33.2 1.0
NE2 B:HIS178 4.1 28.1 1.0
CB B:HIS494 4.2 27.7 1.0
CB B:HIS129 4.2 23.1 1.0
CG B:HIS130 4.2 27.5 1.0
ND1 B:HIS433 4.2 27.1 1.0
CE1 B:HIS382 4.2 39.3 1.0
ND1 B:HIS130 4.3 25.5 1.0
CG B:HIS433 4.3 32.6 1.0
O B:HOH1122 4.3 35.8 1.0
O B:HOH1076 4.3 34.8 1.0
ND1 B:HIS494 4.4 32.2 1.0
ND1 B:HIS129 4.4 33.6 1.0
CE1 B:HIS178 4.4 27.3 1.0
CG B:ASN241 4.6 25.0 1.0
ND2 B:ASN241 4.7 34.7 1.0
NE2 B:HIS326 4.7 29.3 1.0
CG B:HIS494 4.7 31.4 1.0
CG B:HIS129 4.8 26.8 1.0
O B:HIS129 5.0 24.7 1.0

Copper binding site 10 out of 12 in 6rkz

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Copper binding site 10 out of 12 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu709

b:32.2
occ:0.70
 CU4 B:CUZ709 0.0 32.2 0.7
ND1 B:HIS494 2.2 32.2 1.0
S1 B:CUZ709 2.3 33.9 0.9
O B:HOH1122 2.3 35.8 1.0
CU2 B:CUZ709 2.8 25.4 0.5
CU3 B:CUZ709 2.8 25.3 0.6
CG B:HIS494 3.0 31.4 1.0
CB B:HIS494 3.2 27.7 1.0
CU1 B:CUZ709 3.3 35.3 0.7
CE1 B:HIS494 3.3 30.8 1.0
O A:HOH1192 3.5 32.8 1.0
CD2 B:HIS433 3.7 34.8 1.0
NE2 B:HIS433 3.7 33.5 1.0
ND1 B:HIS129 3.7 33.6 1.0
CD2 B:HIS494 4.2 32.2 1.0
CA B:HIS494 4.2 28.2 1.0
NE2 B:HIS494 4.3 31.0 1.0
NZ B:LYS454 4.4 25.8 1.0
CE2 A:PHE621 4.5 25.6 1.0
NE2 B:HIS130 4.6 24.3 1.0
CG B:HIS129 4.6 26.8 1.0
CE1 B:HIS129 4.6 29.9 1.0
CB B:HIS129 4.6 23.1 1.0
CD2 A:PHE621 4.7 33.2 1.0
NE2 B:HIS178 4.7 28.1 1.0
CE B:LYS454 5.0 29.2 1.0
NE2 B:HIS326 5.0 29.3 1.0
C B:HIS494 5.0 30.9 1.0

Reference:

L.Zhang, A.Wust, B.Prasser, C.Muller, O.Einsle. Functional Assembly of Nitrous Oxide Reductase Provides Insights Into Copper Site Maturation. Proc.Natl.Acad.Sci.Usa V. 116 12822 2019.
ISSN: ESSN 1091-6490
PubMed: 31189605
DOI: 10.1073/PNAS.1903819116
Page generated: Wed Jul 31 07:21:47 2024

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