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Copper in PDB 3s0p: Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase

Enzymatic activity of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase

All present enzymatic activity of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase, PDB code: 3s0p was solved by A.Galaleldeen, A.B.Taylor, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.72 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.866, 105.329, 69.660, 90.00, 96.43, 90.00
R / Rfree (%) 20.4 / 24.9

Copper Binding Sites:

The binding sites of Copper atom in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase (pdb code 3s0p). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase, PDB code: 3s0p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3s0p

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Copper binding site 1 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu155

b:37.8
occ:1.00
 NE2 A:HIS48 2.2 33.6 1.0
ND1 A:HIS46 2.3 39.3 1.0
CE1 A:HIS120 2.4 30.8 1.0
NE2 A:HIS120 2.8 32.4 1.0
CE1 A:HIS48 3.0 31.0 1.0
CG A:HIS46 3.0 30.4 1.0
CB A:HIS46 3.0 26.5 1.0
CD2 A:HIS48 3.3 33.4 1.0
ND1 A:HIS120 3.4 33.0 1.0
CE1 A:HIS46 3.5 43.6 1.0
CE1 A:HIS63 3.6 62.9 1.0
NE2 A:HIS63 3.7 60.9 1.0
CD2 A:HIS120 4.0 32.2 1.0
ND1 A:HIS48 4.1 26.3 1.0
CD2 A:HIS46 4.3 35.2 1.0
CG A:HIS120 4.3 32.7 1.0
CG A:HIS48 4.3 25.4 1.0
CB A:VAL118 4.4 20.9 1.0
CG1 A:VAL118 4.4 15.8 1.0
ND1 A:HIS63 4.4 62.3 1.0
CA A:HIS46 4.4 26.7 1.0
NE2 A:HIS46 4.4 46.9 1.0
CD2 A:HIS63 4.5 54.4 1.0
N A:HIS46 4.8 22.9 1.0
CG A:HIS63 4.9 47.1 1.0
O A:VAL118 4.9 24.5 1.0

Copper binding site 2 out of 8 in 3s0p

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Copper binding site 2 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu155

b:43.8
occ:1.00
 NE2 B:HIS48 2.1 37.2 1.0
CE1 B:HIS120 2.3 26.2 1.0
ND1 B:HIS46 2.4 40.6 1.0
NE2 B:HIS120 2.8 39.0 1.0
CE1 B:HIS48 3.0 37.6 1.0
CG B:HIS46 3.0 33.2 1.0
CB B:HIS46 3.1 32.8 1.0
CD2 B:HIS48 3.3 32.4 1.0
ND1 B:HIS120 3.4 31.4 1.0
CE1 B:HIS46 3.5 45.3 1.0
CE1 B:HIS63 3.7 52.5 1.0
NE2 B:HIS63 3.7 57.2 1.0
CD2 B:HIS120 4.0 30.4 1.0
ND1 B:HIS48 4.1 31.6 1.0
CG B:HIS120 4.3 29.6 1.0
CD2 B:HIS46 4.3 33.9 1.0
CG B:HIS48 4.3 27.3 1.0
CB B:VAL118 4.3 19.5 1.0
CG1 B:VAL118 4.4 16.2 1.0
CA B:HIS46 4.4 27.7 1.0
ND1 B:HIS63 4.5 50.9 1.0
NE2 B:HIS46 4.5 43.1 1.0
CD2 B:HIS63 4.5 65.0 1.0
O B:VAL118 4.7 26.8 1.0
N B:HIS46 4.8 27.4 1.0
CG B:HIS63 4.9 47.6 1.0

Copper binding site 3 out of 8 in 3s0p

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Copper binding site 3 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu155

b:50.8
occ:1.00
 NE2 C:HIS48 2.2 38.5 1.0
ND1 C:HIS46 2.3 37.3 1.0
CE1 C:HIS120 2.4 29.5 1.0
NE2 C:HIS120 2.9 33.3 1.0
CG C:HIS46 3.0 32.3 1.0
CE1 C:HIS48 3.0 30.8 1.0
CB C:HIS46 3.0 26.5 1.0
CD2 C:HIS48 3.3 34.9 1.0
CE1 C:HIS46 3.4 42.2 1.0
ND1 C:HIS120 3.5 32.3 1.0
NE2 C:HIS63 3.5 60.3 1.0
CE1 C:HIS63 3.6 57.6 1.0
CD2 C:HIS120 4.1 31.5 1.0
ND1 C:HIS48 4.1 29.5 1.0
CD2 C:HIS46 4.2 36.0 1.0
ND1 C:HIS63 4.3 64.0 1.0
CD2 C:HIS63 4.3 64.3 1.0
CG C:HIS48 4.3 26.4 1.0
CG C:HIS120 4.4 30.1 1.0
NE2 C:HIS46 4.4 42.4 1.0
CA C:HIS46 4.4 26.8 1.0
CB C:VAL118 4.5 21.1 1.0
CG1 C:VAL118 4.6 15.6 1.0
CG C:HIS63 4.7 56.2 1.0
N C:HIS46 4.9 26.9 1.0
O C:VAL118 5.0 33.3 1.0

Copper binding site 4 out of 8 in 3s0p

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Copper binding site 4 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu155

b:50.7
occ:1.00
 NE2 D:HIS48 2.2 30.1 1.0
ND1 D:HIS46 2.3 36.1 1.0
CE1 D:HIS120 2.4 26.9 1.0
NE2 D:HIS120 2.8 35.8 1.0
CE1 D:HIS48 3.0 30.2 1.0
CG D:HIS46 3.0 31.6 1.0
CB D:HIS46 3.1 31.0 1.0
CD2 D:HIS48 3.3 30.2 1.0
CE1 D:HIS46 3.4 41.6 1.0
ND1 D:HIS120 3.4 28.1 1.0
NE2 D:HIS63 3.6 52.3 1.0
CE1 D:HIS63 3.7 52.6 1.0
CD2 D:HIS120 4.0 36.0 1.0
ND1 D:HIS48 4.1 27.8 1.0
CD2 D:HIS46 4.2 35.6 1.0
CG D:HIS120 4.3 29.4 1.0
CG D:HIS48 4.3 28.8 1.0
CD2 D:HIS63 4.4 69.5 1.0
NE2 D:HIS46 4.4 46.6 1.0
CG1 D:VAL118 4.5 15.4 1.0
ND1 D:HIS63 4.5 56.4 1.0
CB D:VAL118 4.5 19.9 1.0
CA D:HIS46 4.5 30.5 1.0
N D:HIS46 4.8 25.8 1.0
CG D:HIS63 4.9 54.0 1.0
O D:VAL118 5.0 34.5 1.0

Copper binding site 5 out of 8 in 3s0p

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Copper binding site 5 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu155

b:48.0
occ:1.00
 NE2 E:HIS48 2.2 34.3 1.0
CE1 E:HIS120 2.4 25.1 1.0
ND1 E:HIS46 2.4 38.2 1.0
NE2 E:HIS120 2.7 31.4 1.0
CE1 E:HIS48 2.8 37.5 1.0
CG E:HIS46 3.2 30.3 1.0
CB E:HIS46 3.3 25.9 1.0
NE2 E:HIS63 3.4 57.1 1.0
CD2 E:HIS48 3.4 32.4 1.0
CE1 E:HIS46 3.5 43.3 1.0
ND1 E:HIS120 3.5 28.4 1.0
CE1 E:HIS63 3.5 51.0 1.0
CD2 E:HIS120 3.9 28.5 1.0
ND1 E:HIS48 4.1 23.3 1.0
CD2 E:HIS63 4.2 62.4 1.0
CG E:HIS120 4.3 30.6 1.0
ND1 E:HIS63 4.4 55.4 1.0
CD2 E:HIS46 4.4 34.1 1.0
CG E:HIS48 4.4 25.6 1.0
NE2 E:HIS46 4.5 49.3 1.0
CG1 E:VAL118 4.6 14.9 1.0
CB E:VAL118 4.6 18.1 1.0
CA E:HIS46 4.7 26.5 1.0
CG E:HIS63 4.8 47.0 1.0

Copper binding site 6 out of 8 in 3s0p

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Copper binding site 6 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu155

b:50.3
occ:1.00
 NE2 F:HIS48 2.2 34.0 1.0
CE1 F:HIS120 2.2 24.6 1.0
ND1 F:HIS46 2.3 34.8 1.0
NE2 F:HIS120 2.7 29.8 1.0
CG F:HIS46 3.0 32.0 1.0
CB F:HIS46 3.0 32.7 1.0
CE1 F:HIS48 3.0 33.4 1.0
CD2 F:HIS48 3.3 36.4 1.0
ND1 F:HIS120 3.3 33.5 1.0
CE1 F:HIS46 3.4 38.4 1.0
NE2 F:HIS63 3.7 61.0 1.0
CE1 F:HIS63 3.7 52.6 1.0
CD2 F:HIS120 3.9 32.5 1.0
CG F:HIS120 4.2 30.8 1.0
ND1 F:HIS48 4.2 28.9 1.0
CD2 F:HIS46 4.2 34.6 1.0
CG1 F:VAL118 4.3 15.4 1.0
CG F:HIS48 4.4 26.7 1.0
NE2 F:HIS46 4.4 42.9 1.0
CB F:VAL118 4.4 21.0 1.0
CA F:HIS46 4.4 26.8 1.0
ND1 F:HIS63 4.5 55.1 1.0
CD2 F:HIS63 4.5 62.6 1.0
N F:HIS46 4.8 25.1 1.0
O F:VAL118 4.8 29.9 1.0
CG F:HIS63 5.0 52.7 1.0
C F:HIS46 5.0 25.5 1.0

Copper binding site 7 out of 8 in 3s0p

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Copper binding site 7 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu155

b:51.8
occ:1.00
 CE1 G:HIS120 2.0 29.7 1.0
NE2 G:HIS48 2.3 37.7 1.0
ND1 G:HIS46 2.3 37.7 1.0
NE2 G:HIS120 2.7 37.8 1.0
CG G:HIS46 3.1 29.4 1.0
ND1 G:HIS120 3.1 34.3 1.0
CE1 G:HIS48 3.1 35.4 1.0
CB G:HIS46 3.2 33.3 1.0
CD2 G:HIS48 3.4 33.9 1.0
CE1 G:HIS46 3.4 43.0 1.0
NE2 G:HIS63 3.8 57.5 1.0
CE1 G:HIS63 3.8 57.9 1.0
CD2 G:HIS120 3.9 27.7 1.0
CG G:HIS120 4.1 27.6 1.0
ND1 G:HIS48 4.3 30.9 1.0
CD2 G:HIS46 4.3 31.6 1.0
CB G:VAL118 4.3 19.4 1.0
CG1 G:VAL118 4.3 15.0 1.0
NE2 G:HIS46 4.4 50.2 1.0
CG G:HIS48 4.5 26.4 1.0
CA G:HIS46 4.5 30.8 1.0
ND1 G:HIS63 4.7 65.0 1.0
CD2 G:HIS63 4.7 63.4 1.0
N G:HIS46 4.7 28.4 1.0
O G:VAL118 4.8 30.8 1.0

Copper binding site 8 out of 8 in 3s0p

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Copper binding site 8 out of 8 in the Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu155

b:43.9
occ:1.00
 NE2 H:HIS48 2.2 29.0 1.0
CE1 H:HIS120 2.3 28.4 1.0
ND1 H:HIS46 2.3 37.3 1.0
NE2 H:HIS120 2.7 36.5 1.0
CE1 H:HIS48 2.9 32.4 1.0
CG H:HIS46 3.1 29.9 1.0
CB H:HIS46 3.1 29.1 1.0
CD2 H:HIS48 3.4 35.6 1.0
ND1 H:HIS120 3.4 27.6 1.0
CE1 H:HIS46 3.5 38.4 1.0
NE2 H:HIS63 3.5 56.6 1.0
CE1 H:HIS63 3.6 56.6 1.0
CD2 H:HIS120 3.9 33.2 1.0
ND1 H:HIS48 4.1 26.9 1.0
CG H:HIS120 4.3 31.1 1.0
CD2 H:HIS46 4.3 32.0 1.0
CD2 H:HIS63 4.3 68.6 1.0
CG H:HIS48 4.4 26.4 1.0
ND1 H:HIS63 4.4 63.4 1.0
NE2 H:HIS46 4.4 39.4 1.0
CG1 H:VAL118 4.5 14.7 1.0
CB H:VAL118 4.5 16.7 1.0
CA H:HIS46 4.6 28.8 1.0
CG H:HIS63 4.8 56.5 1.0

Reference:

A.Galaleldeen, A.B.Taylor, P.J.Hart. Biophysical Properties of Tomato Chloroplast Sod To Be Published.
Page generated: Sun Dec 13 11:11:37 2020

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