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Copper in PDB 3sbq: Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form:
1.7.99.6;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form, PDB code: 3sbq was solved by A.Pomowski, W.G.Zumft, 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) 50.00 / 1.70
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 70.373, 70.373, 400.104, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.3

Other elements in 3sbq:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form also contains other interesting chemical elements:

Potassium (K) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 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, P65 Crystal Form (pdb code 3sbq). 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, P65 Crystal Form, PDB code: 3sbq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 3sbq

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Copper binding site 1 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:28.2
occ:1.00
 CU1 A:CUA701 0.0 28.2 1.0
SG A:CYS618 2.3 20.4 1.0
SD A:MET629 2.3 23.6 1.0
SG A:CYS622 2.4 25.0 1.0
CU2 A:CUA701 2.6 29.5 1.0
CB A:CYS618 3.2 20.1 1.0
CE A:MET629 3.2 22.7 1.0
CB A:CYS622 3.4 23.8 1.0
CG A:MET629 3.6 22.8 1.0
CD2 A:HIS583 3.7 28.7 1.0
O A:TRP620 3.9 23.7 1.0
CG A:HIS583 4.0 26.3 1.0
CB A:MET629 4.1 21.7 1.0
CB A:HIS583 4.2 21.6 1.0
CA A:HIS583 4.4 22.0 1.0
NE2 A:HIS583 4.5 28.8 1.0
ND1 A:HIS626 4.5 20.8 1.0
CA A:CYS618 4.6 19.9 1.0
O A:SER582 4.8 21.9 1.0
CA A:CYS622 4.8 24.0 1.0
N A:GLY584 4.9 20.8 1.0
CB A:ALA552 4.9 28.0 1.0
ND1 A:HIS583 5.0 28.5 1.0

Copper binding site 2 out of 12 in 3sbq

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Copper binding site 2 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:29.5
occ:1.00
 CU2 A:CUA701 0.0 29.5 1.0
ND1 A:HIS626 2.0 20.8 1.0
O A:TRP620 2.4 23.7 1.0
SG A:CYS622 2.5 25.0 1.0
CU1 A:CUA701 2.6 28.2 1.0
SG A:CYS618 2.7 20.4 1.0
CE1 A:HIS626 2.7 21.8 1.0
CG A:HIS626 3.1 23.5 1.0
CB A:CYS622 3.4 23.8 1.0
N A:CYS622 3.4 23.8 1.0
C A:TRP620 3.5 23.6 1.0
CB A:CYS618 3.7 20.1 1.0
CB A:HIS626 3.7 24.1 1.0
CA A:HIS626 3.8 24.0 1.0
CA A:PHE621 3.9 24.0 1.0
NE2 A:HIS626 3.9 25.8 1.0
CA A:CYS622 4.0 24.0 1.0
C A:PHE621 4.0 23.5 1.0
O A:CYS618 4.1 20.3 1.0
N A:PHE621 4.1 24.0 1.0
CD2 A:HIS626 4.1 25.4 1.0
O A:HIS626 4.3 24.1 1.0
SD A:MET629 4.3 23.6 1.0
N A:TRP620 4.4 23.0 1.0
C A:CYS618 4.4 21.1 1.0
C A:HIS626 4.5 24.3 1.0
CA A:TRP620 4.5 23.9 1.0
CB A:MET629 4.7 21.7 1.0
CA A:CYS618 4.7 19.9 1.0
O A:HOH815 4.8 31.7 1.0
N A:HIS623 4.8 24.9 1.0
C A:CYS622 4.9 24.8 1.0

Copper binding site 3 out of 12 in 3sbq

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Copper binding site 3 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:38.8
occ:0.80
 CU1 A:CUK702 0.0 38.8 0.8
S1 A:CUK702 2.3 37.4 0.8
ND1 A:HIS494 2.3 33.3 1.0
S2 A:CUK702 2.5 43.8 0.8
CU2 A:CUK702 2.8 38.0 0.8
CU3 A:CUK702 2.9 33.8 0.8
CG A:HIS494 3.1 32.3 1.0
CB A:HIS494 3.2 30.1 1.0
NE2 A:HIS433 3.3 32.7 1.0
CU4 A:CUK702 3.3 43.0 0.8
CE1 A:HIS494 3.4 34.0 1.0
CD2 A:HIS433 3.5 32.2 1.0
ND1 A:HIS129 3.9 30.0 1.0
CA A:HIS494 4.2 28.8 1.0
CD2 A:HIS494 4.3 32.9 1.0
NE2 A:HIS494 4.5 33.4 1.0
NZ A:LYS454 4.5 29.7 1.0
NE2 A:HIS130 4.6 19.0 1.0
CE1 A:HIS433 4.6 31.4 1.0
CE2 B:PHE621 4.7 29.5 1.0
NE2 A:HIS178 4.7 28.6 1.0
CB A:HIS129 4.7 23.6 1.0
CD2 B:PHE621 4.8 27.4 1.0
CG A:HIS129 4.8 24.6 1.0
CG A:HIS433 4.8 28.4 1.0
NE2 A:HIS326 4.9 26.9 1.0
CE1 A:HIS129 4.9 28.1 1.0
C A:HIS494 4.9 28.2 1.0
NE2 A:HIS382 4.9 32.5 1.0

Copper binding site 4 out of 12 in 3sbq

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Copper binding site 4 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:38.0
occ:0.80
 CU2 A:CUK702 0.0 38.0 0.8
NE2 A:HIS178 2.0 28.6 1.0
S1 A:CUK702 2.2 37.4 0.8
CU3 A:CUK702 2.8 33.8 0.8
ND1 A:HIS129 2.8 30.0 1.0
CU1 A:CUK702 2.8 38.8 0.8
CE1 A:HIS178 2.9 28.5 1.0
CD2 A:HIS178 3.0 27.5 1.0
CG A:HIS129 3.3 24.6 1.0
CE1 A:HIS130 3.4 18.6 1.0
NE2 A:HIS130 3.4 19.0 1.0
CB A:HIS129 3.5 23.6 1.0
CE1 A:HIS129 3.6 28.1 1.0
ND1 A:HIS494 3.8 33.3 1.0
ND1 A:HIS178 3.9 29.1 1.0
CG A:HIS178 4.0 26.1 1.0
CD2 A:HIS129 4.3 25.8 1.0
CE1 A:HIS494 4.4 34.0 1.0
CG A:HIS494 4.4 32.3 1.0
NE2 A:HIS129 4.4 27.0 1.0
NE2 A:HIS433 4.5 32.7 1.0
ND1 A:HIS130 4.5 19.2 1.0
CD2 A:HIS130 4.6 22.2 1.0
CU4 A:CUK702 4.6 43.0 0.8
CB A:HIS494 4.7 30.1 1.0
CE B:MET627 4.9 30.7 1.0
CA A:HIS129 5.0 23.2 1.0

Copper binding site 5 out of 12 in 3sbq

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Copper binding site 5 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:33.8
occ:0.80
 CU3 A:CUK702 0.0 33.8 0.8
NE2 A:HIS433 1.9 32.7 1.0
NE2 A:HIS130 2.1 19.0 1.0
S1 A:CUK702 2.2 37.4 0.8
CE1 A:HIS433 2.7 31.4 1.0
CU2 A:CUK702 2.8 38.0 0.8
CU1 A:CUK702 2.9 38.8 0.8
CD2 A:HIS130 3.0 22.2 1.0
CE1 A:HIS130 3.1 18.6 1.0
CD2 A:HIS433 3.1 32.2 1.0
CU4 A:CUK702 3.3 43.0 0.8
ND2 A:ASN241 3.7 32.2 1.0
ND1 A:HIS433 3.9 30.3 1.0
CG A:HIS433 4.1 28.4 1.0
ND1 A:HIS130 4.1 19.2 1.0
CG A:HIS130 4.1 21.1 1.0
CE1 A:HIS382 4.2 32.0 1.0
NE2 A:HIS382 4.2 32.5 1.0
NE2 A:HIS178 4.2 28.6 1.0
CB A:HIS129 4.3 23.6 1.0
S2 A:CUK702 4.3 43.8 0.8
CB A:HIS494 4.3 30.1 1.0
CE1 A:HIS178 4.4 28.5 1.0
OD1 A:ASN241 4.4 32.2 1.0
NE2 A:HIS326 4.5 26.9 1.0
CG A:ASN241 4.5 27.5 1.0
ND1 A:HIS494 4.7 33.3 1.0
CE1 A:HIS326 4.8 29.3 1.0
ND1 A:HIS129 4.8 30.0 1.0
O A:HIS129 4.9 21.9 1.0
CG A:HIS494 4.9 32.3 1.0
CG A:HIS129 5.0 24.6 1.0

Copper binding site 6 out of 12 in 3sbq

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Copper binding site 6 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:43.0
occ:0.80
 CU4 A:CUK702 0.0 43.0 0.8
NE2 A:HIS326 1.9 26.9 1.0
NE2 A:HIS382 2.1 32.5 1.0
S1 A:CUK702 2.4 37.4 0.8
S2 A:CUK702 2.6 43.8 0.8
CE1 A:HIS326 2.8 29.3 1.0
CE1 A:HIS382 2.9 32.0 1.0
CD2 A:HIS326 3.0 27.8 1.0
CD2 A:HIS382 3.3 31.4 1.0
NE2 A:HIS433 3.3 32.7 1.0
CU3 A:CUK702 3.3 33.8 0.8
CU1 A:CUK702 3.3 38.8 0.8
CD2 A:HIS433 3.6 32.2 1.0
ND1 A:HIS326 3.9 28.1 1.0
CE1 A:HIS433 4.0 31.4 1.0
CG A:HIS326 4.0 25.9 1.0
ND1 A:HIS382 4.1 31.9 1.0
CG A:HIS382 4.3 26.9 1.0
CG A:HIS433 4.3 28.4 1.0
OD1 A:ASN241 4.4 32.2 1.0
ND1 A:HIS433 4.5 30.3 1.0
CU2 A:CUK702 4.6 38.0 0.8
N A:HIS433 4.8 24.1 1.0
CE2 B:PHE621 4.9 29.5 1.0

Copper binding site 7 out of 12 in 3sbq

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Copper binding site 7 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:32.8
occ:1.00
 CU1 B:CUA701 0.0 32.8 1.0
ND1 B:HIS626 1.9 20.9 1.0
O B:TRP620 2.4 24.6 1.0
SG B:CYS622 2.5 25.5 1.0
CU2 B:CUA701 2.6 29.7 1.0
CE1 B:HIS626 2.7 23.9 1.0
SG B:CYS618 2.8 23.0 1.0
CG B:HIS626 3.0 24.2 1.0
N B:CYS622 3.3 25.7 1.0
CB B:CYS622 3.4 25.7 1.0
C B:TRP620 3.4 24.4 1.0
CB B:HIS626 3.5 25.1 1.0
CB B:CYS618 3.7 20.3 1.0
CA B:HIS626 3.9 25.5 1.0
CA B:PHE621 3.9 24.8 1.0
NE2 B:HIS626 3.9 25.4 1.0
CA B:CYS622 3.9 25.5 1.0
C B:PHE621 4.0 25.0 1.0
CD2 B:HIS626 4.1 24.0 1.0
O B:CYS618 4.1 21.6 1.0
N B:PHE621 4.1 24.9 1.0
O B:HIS626 4.2 26.6 1.0
SD B:MET629 4.4 24.1 1.0
N B:TRP620 4.4 23.5 1.0
C B:CYS618 4.5 20.5 1.0
C B:HIS626 4.5 25.1 1.0
CA B:TRP620 4.5 24.6 1.0
CB B:MET629 4.7 23.0 1.0
CA B:CYS618 4.8 20.7 1.0
O B:HOH844 4.8 29.4 1.0
C B:CYS622 4.8 25.7 1.0
N B:HIS623 4.8 25.7 1.0

Copper binding site 8 out of 12 in 3sbq

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Copper binding site 8 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:29.7
occ:1.00
 CU2 B:CUA701 0.0 29.7 1.0
SG B:CYS618 2.2 23.0 1.0
SG B:CYS622 2.4 25.5 1.0
SD B:MET629 2.4 24.1 1.0
CU1 B:CUA701 2.6 32.8 1.0
CE B:MET629 3.1 21.3 1.0
CB B:CYS618 3.2 20.3 1.0
CB B:CYS622 3.4 25.7 1.0
CG B:MET629 3.7 24.6 1.0
CD2 B:HIS583 3.8 28.1 1.0
O B:TRP620 3.9 24.6 1.0
CG B:HIS583 4.0 26.2 1.0
CB B:HIS583 4.1 23.5 1.0
CB B:MET629 4.1 23.0 1.0
CA B:HIS583 4.3 23.6 1.0
ND1 B:HIS626 4.5 20.9 1.0
CA B:CYS618 4.6 20.7 1.0
NE2 B:HIS583 4.7 28.9 1.0
CA B:CYS622 4.7 25.5 1.0
O B:SER582 4.7 23.7 1.0
N B:GLY584 4.9 22.5 1.0
N B:CYS622 4.9 25.7 1.0

Copper binding site 9 out of 12 in 3sbq

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Copper binding site 9 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:41.6
occ:0.80
 CU1 B:CUK702 0.0 41.6 0.8
S1 B:CUK702 2.3 41.9 0.8
S2 B:CUK702 2.5 45.8 0.8
ND1 B:HIS494 2.7 37.0 1.0
CU2 B:CUK702 2.8 39.5 0.8
CU3 B:CUK702 3.0 39.6 0.8
CB B:HIS494 3.2 30.6 1.0
CG B:HIS494 3.3 33.9 1.0
CU4 B:CUK702 3.4 44.8 0.8
CE1 B:HIS494 3.8 37.0 1.0
CD2 B:HIS433 3.9 34.9 1.0
CD2 B:HIS129 3.9 26.2 1.0
NE2 B:HIS433 4.0 34.8 1.0
CA B:HIS494 4.2 29.6 1.0
NZ B:LYS454 4.4 24.9 1.0
CD2 B:HIS494 4.5 35.6 1.0
CE2 A:PHE621 4.5 28.2 1.0
CD2 A:PHE621 4.6 27.4 1.0
NE2 B:HIS178 4.6 27.4 1.0
NE2 B:HIS130 4.6 21.7 1.0
NE2 B:HIS494 4.7 36.2 1.0
CG B:HIS129 4.7 24.9 1.0
C B:HIS494 4.7 28.8 1.0
CB B:HIS129 4.8 22.5 1.0
NE2 B:HIS326 4.8 26.7 1.0
O B:HOH859 4.8 31.3 1.0
O B:HIS494 4.9 28.1 1.0
CG B:HIS433 5.0 28.7 1.0
NE2 B:HIS129 5.0 26.7 1.0

Copper binding site 10 out of 12 in 3sbq

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Copper binding site 10 out of 12 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal Form


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, P65 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:39.5
occ:0.80
 CU2 B:CUK702 0.0 39.5 0.8
NE2 B:HIS178 2.0 27.4 1.0
S1 B:CUK702 2.2 41.9 0.8
CD2 B:HIS129 2.5 26.2 1.0
CU3 B:CUK702 2.8 39.6 0.8
CU1 B:CUK702 2.8 41.6 0.8
CE1 B:HIS178 2.9 28.5 1.0
CD2 B:HIS178 2.9 25.3 1.0
CG B:HIS129 3.1 24.9 1.0
NE2 B:HIS130 3.3 21.7 1.0
CB B:HIS129 3.4 22.5 1.0
CE1 B:HIS130 3.5 21.2 1.0
NE2 B:HIS129 3.6 26.7 1.0
ND1 B:HIS178 4.0 26.6 1.0
ND1 B:HIS494 4.0 37.0 1.0
CG B:HIS178 4.0 25.3 1.0
ND1 B:HIS129 4.2 27.1 1.0
CG B:HIS494 4.3 33.9 1.0
CD2 B:HIS130 4.4 21.9 1.0
CE1 B:HIS129 4.4 24.1 1.0
CB B:HIS494 4.5 30.6 1.0
CU4 B:CUK702 4.6 44.8 0.8
ND1 B:HIS130 4.6 19.9 1.0
CE1 B:HIS494 4.6 37.0 1.0
CA B:HIS129 4.8 22.8 1.0
NE2 B:HIS433 5.0 34.8 1.0
ND2 B:ASN241 5.0 31.8 1.0

Reference:

A.Pomowski, W.G.Zumft, P.M.Kroneck, O.Einsle. N2O Binding at A [4CU:2S] Copper-Sulphur Cluster in Nitrous Oxide Reductase. Nature V. 477 234 2011.
ISSN: ISSN 0028-0836
PubMed: 21841804
DOI: 10.1038/NATURE10332
Page generated: Wed Jul 31 01:43:50 2024

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