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Copper in PDB 1to4: Structure of the Cytosolic Cu,Zn Sod From S. Mansoni

Enzymatic activity of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni

All present enzymatic activity of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni:
1.15.1.1;

Protein crystallography data

The structure of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni, PDB code: 1to4 was solved by R.M.F.Cardoso, C.H.T.P.Silva, A.P.Ulian De Araujo, T.Tanaka, M.Tanaka, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.270, 95.080, 78.410, 90.00, 103.55, 90.00
R / Rfree (%) 15.7 / 17.1

Other elements in 1to4:

The structure of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni (pdb code 1to4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni, PDB code: 1to4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 1to4

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Copper binding site 1 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:9.4
occ:0.16
 CU A:CU801 0.0 9.4 0.2
CU A:CU801 1.0 9.6 0.8
ND1 A:HIS45 2.1 6.3 1.0
NE2 A:HIS47 2.2 4.4 1.0
NE2 A:HIS62 2.3 8.2 1.0
NE2 A:HIS119 2.3 7.2 1.0
O A:HOH847 2.8 10.1 0.3
CE1 A:HIS45 2.8 7.5 1.0
O A:HOH847 2.8 10.2 0.7
CE1 A:HIS47 2.9 6.5 1.0
CD2 A:HIS62 2.9 8.2 1.0
CG A:HIS45 3.1 5.7 1.0
CE1 A:HIS119 3.1 6.0 1.0
CE1 A:HIS62 3.3 8.0 1.0
CD2 A:HIS119 3.3 6.2 1.0
CD2 A:HIS47 3.4 5.2 1.0
CB A:HIS45 3.6 7.3 1.0
NE2 A:HIS45 3.9 5.7 1.0
CG A:HIS62 4.1 6.3 1.0
CD2 A:HIS45 4.1 6.3 1.0
ND1 A:HIS47 4.1 6.2 1.0
ND1 A:HIS62 4.2 5.4 1.0
ND1 A:HIS119 4.2 5.7 1.0
CG A:HIS47 4.4 5.1 1.0
CG A:HIS119 4.4 6.5 1.0
CA A:HIS45 4.8 5.2 1.0
O A:HOH862 4.8 18.1 1.0
N A:HIS45 4.8 5.0 1.0
O A:HOH863 4.8 19.8 1.0
CB A:VAL117 4.9 5.5 1.0
CG1 A:VAL117 4.9 7.1 1.0

Copper binding site 2 out of 8 in 1to4

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Copper binding site 2 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:9.6
occ:0.84
 CU A:CU801 0.0 9.6 0.8
CU A:CU801 1.0 9.4 0.2
NE2 A:HIS47 1.9 4.4 1.0
NE2 A:HIS119 2.0 7.2 1.0
ND1 A:HIS45 2.1 6.3 1.0
CE1 A:HIS47 2.9 6.5 1.0
CD2 A:HIS119 2.9 6.2 1.0
CD2 A:HIS47 3.0 5.2 1.0
CG A:HIS45 3.0 5.7 1.0
CE1 A:HIS45 3.0 7.5 1.0
CE1 A:HIS119 3.1 6.0 1.0
NE2 A:HIS62 3.2 8.2 1.0
CB A:HIS45 3.3 7.3 1.0
O A:HOH847 3.5 10.1 0.3
O A:HOH847 3.6 10.2 0.7
CD2 A:HIS62 3.7 8.2 1.0
CB A:VAL117 3.9 5.5 1.0
ND1 A:HIS47 4.0 6.2 1.0
CG A:HIS47 4.1 5.1 1.0
CG A:HIS119 4.1 6.5 1.0
CG1 A:VAL117 4.1 7.1 1.0
N A:HIS45 4.1 5.0 1.0
ND1 A:HIS119 4.1 5.7 1.0
CE1 A:HIS62 4.1 8.0 1.0
NE2 A:HIS45 4.2 5.7 1.0
CD2 A:HIS45 4.2 6.3 1.0
CA A:HIS45 4.3 5.2 1.0
O A:VAL117 4.3 5.6 1.0
O A:HIS45 4.6 5.0 1.0
C A:HIS45 4.7 5.4 1.0
CG2 A:VAL117 4.7 7.1 1.0
CG A:HIS62 4.7 6.3 1.0
C A:VAL117 4.8 5.8 1.0
ND1 A:HIS62 4.9 5.4 1.0
CA A:VAL117 5.0 6.5 1.0

Copper binding site 3 out of 8 in 1to4

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Copper binding site 3 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu811

b:9.2
occ:0.14
 CU B:CU811 0.0 9.2 0.1
CU B:CU811 0.9 9.2 0.9
ND1 B:HIS45 1.9 4.5 1.0
NE2 B:HIS119 2.2 3.3 1.0
NE2 B:HIS47 2.3 4.5 1.0
NE2 B:HIS62 2.5 7.9 1.0
O B:HOH861 2.7 11.9 0.3
CE1 B:HIS45 2.7 5.6 1.0
O B:HOH861 2.8 11.9 0.7
CE1 B:HIS47 3.0 5.3 1.0
CG B:HIS45 3.0 4.0 1.0
CE1 B:HIS119 3.1 6.1 1.0
CD2 B:HIS62 3.1 5.8 1.0
CD2 B:HIS119 3.2 5.0 1.0
CD2 B:HIS47 3.4 5.5 1.0
CE1 B:HIS62 3.4 7.4 1.0
CB B:HIS45 3.6 5.6 1.0
NE2 B:HIS45 3.8 6.6 1.0
CD2 B:HIS45 4.0 6.5 1.0
CG B:HIS62 4.1 5.5 1.0
ND1 B:HIS119 4.1 6.2 1.0
ND1 B:HIS47 4.2 5.8 1.0
ND1 B:HIS62 4.2 4.7 1.0
CG B:HIS119 4.3 4.3 1.0
CG B:HIS47 4.4 5.2 1.0
O B:HOH843 4.7 16.2 1.0
N B:HIS45 4.7 3.9 1.0
CA B:HIS45 4.7 4.8 1.0
CB B:VAL117 4.8 3.7 1.0
CG1 B:VAL117 4.9 5.6 1.0

Copper binding site 4 out of 8 in 1to4

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Copper binding site 4 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu811

b:9.2
occ:0.86
 CU B:CU811 0.0 9.2 0.9
CU B:CU811 0.9 9.2 0.1
NE2 B:HIS47 2.0 4.5 1.0
NE2 B:HIS119 2.0 3.3 1.0
ND1 B:HIS45 2.0 4.5 1.0
CD2 B:HIS119 2.9 5.0 1.0
CD2 B:HIS47 3.0 5.5 1.0
CE1 B:HIS47 3.0 5.3 1.0
CE1 B:HIS45 3.0 5.6 1.0
CE1 B:HIS119 3.0 6.1 1.0
CG B:HIS45 3.1 4.0 1.0
O B:HOH861 3.3 11.9 0.3
NE2 B:HIS62 3.3 7.9 1.0
CB B:HIS45 3.4 5.6 1.0
O B:HOH861 3.5 11.9 0.7
CD2 B:HIS62 3.7 5.8 1.0
CB B:VAL117 4.0 3.7 1.0
ND1 B:HIS47 4.1 5.8 1.0
CG B:HIS119 4.1 4.3 1.0
CG B:HIS47 4.1 5.2 1.0
ND1 B:HIS119 4.1 6.2 1.0
NE2 B:HIS45 4.1 6.6 1.0
CD2 B:HIS45 4.2 6.5 1.0
CG1 B:VAL117 4.2 5.6 1.0
N B:HIS45 4.2 3.9 1.0
CE1 B:HIS62 4.2 7.4 1.0
CA B:HIS45 4.3 4.8 1.0
O B:VAL117 4.3 5.3 1.0
O B:HIS45 4.6 4.1 1.0
C B:HIS45 4.7 4.7 1.0
CG B:HIS62 4.7 5.5 1.0
CG2 B:VAL117 4.7 5.3 1.0
C B:VAL117 4.8 3.8 1.0
ND1 B:HIS62 4.9 4.7 1.0
CA B:VAL117 5.0 3.5 1.0

Copper binding site 5 out of 8 in 1to4

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Copper binding site 5 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu821

b:12.6
occ:0.16
 CU C:CU821 0.0 12.6 0.2
CU C:CU821 1.0 12.5 0.8
ND1 C:HIS45 2.0 6.5 1.0
NE2 C:HIS47 2.3 5.4 1.0
NE2 C:HIS62 2.3 8.1 1.0
NE2 C:HIS119 2.3 8.8 1.0
CE1 C:HIS45 2.8 7.9 1.0
O C:HOH890 2.9 11.9 0.7
CE1 C:HIS47 2.9 7.1 1.0
CD2 C:HIS62 2.9 9.7 1.0
O C:HOH890 3.0 11.8 0.3
CG C:HIS45 3.1 7.5 1.0
CE1 C:HIS119 3.1 8.6 1.0
CE1 C:HIS62 3.3 7.2 1.0
CD2 C:HIS119 3.3 7.5 1.0
CD2 C:HIS47 3.4 6.4 1.0
CB C:HIS45 3.6 8.2 1.0
NE2 C:HIS45 3.9 6.6 1.0
CG C:HIS62 4.0 7.0 1.0
CD2 C:HIS45 4.0 6.6 1.0
ND1 C:HIS47 4.1 7.9 1.0
ND1 C:HIS62 4.1 7.2 1.0
ND1 C:HIS119 4.2 8.1 1.0
CG C:HIS119 4.4 7.7 1.0
CG C:HIS47 4.4 7.0 1.0
O C:HOH898 4.7 19.2 1.0
CA C:HIS45 4.8 7.2 1.0
O C:HOH883 4.8 20.5 1.0
N C:HIS45 4.8 6.4 1.0
CB C:VAL117 4.9 6.8 1.0
CG1 C:VAL117 5.0 9.5 1.0

Copper binding site 6 out of 8 in 1to4

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Copper binding site 6 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu821

b:12.5
occ:0.84
 CU C:CU821 0.0 12.5 0.8
CU C:CU821 1.0 12.6 0.2
NE2 C:HIS47 2.0 5.4 1.0
NE2 C:HIS119 2.0 8.8 1.0
ND1 C:HIS45 2.1 6.5 1.0
CE1 C:HIS47 2.9 7.1 1.0
CD2 C:HIS119 3.0 7.5 1.0
CD2 C:HIS47 3.0 6.4 1.0
CE1 C:HIS45 3.0 7.9 1.0
CG C:HIS45 3.0 7.5 1.0
CE1 C:HIS119 3.1 8.6 1.0
NE2 C:HIS62 3.2 8.1 1.0
CB C:HIS45 3.3 8.2 1.0
O C:HOH890 3.6 11.9 0.7
CD2 C:HIS62 3.7 9.7 1.0
O C:HOH890 3.7 11.8 0.3
CB C:VAL117 4.0 6.8 1.0
ND1 C:HIS47 4.0 7.9 1.0
CG C:HIS47 4.1 7.0 1.0
CE1 C:HIS62 4.1 7.2 1.0
CG C:HIS119 4.1 7.7 1.0
N C:HIS45 4.1 6.4 1.0
NE2 C:HIS45 4.1 6.6 1.0
ND1 C:HIS119 4.1 8.1 1.0
CG1 C:VAL117 4.1 9.5 1.0
CD2 C:HIS45 4.2 6.6 1.0
CA C:HIS45 4.3 7.2 1.0
O C:VAL117 4.3 7.6 1.0
O C:HIS45 4.5 7.7 1.0
C C:HIS45 4.6 7.2 1.0
CG2 C:VAL117 4.7 8.1 1.0
CG C:HIS62 4.7 7.0 1.0
C C:VAL117 4.8 7.3 1.0
ND1 C:HIS62 4.9 7.2 1.0
CA C:VAL117 5.0 7.2 1.0

Copper binding site 7 out of 8 in 1to4

Go back to Copper Binding Sites List in 1to4
Copper binding site 7 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu831

b:12.2
occ:0.13
 CU D:CU831 0.0 12.2 0.1
CU D:CU831 0.9 12.2 0.9
ND1 D:HIS45 1.8 7.0 1.0
NE2 D:HIS47 2.3 6.3 1.0
NE2 D:HIS119 2.4 7.9 1.0
NE2 D:HIS62 2.4 9.1 1.0
CE1 D:HIS45 2.6 8.2 1.0
O D:HOH852 2.7 11.7 0.2
O D:HOH852 2.9 11.8 0.8
CG D:HIS45 2.9 7.7 1.0
CD2 D:HIS62 3.0 8.7 1.0
CE1 D:HIS47 3.0 7.5 1.0
CE1 D:HIS119 3.2 9.6 1.0
CD2 D:HIS119 3.3 8.0 1.0
CE1 D:HIS62 3.3 8.7 1.0
CD2 D:HIS47 3.3 6.5 1.0
CB D:HIS45 3.4 8.5 1.0
NE2 D:HIS45 3.7 8.8 1.0
CD2 D:HIS45 3.9 9.3 1.0
CG D:HIS62 4.0 7.7 1.0
ND1 D:HIS62 4.1 6.1 1.0
ND1 D:HIS47 4.2 7.5 1.0
ND1 D:HIS119 4.3 10.0 1.0
CG D:HIS47 4.4 7.5 1.0
CG D:HIS119 4.4 8.6 1.0
N D:HIS45 4.6 7.6 1.0
CA D:HIS45 4.6 6.8 1.0
O D:HOH876 4.7 18.4 1.0
CB D:VAL117 4.8 6.8 1.0
CG1 D:VAL117 4.9 8.2 1.0

Copper binding site 8 out of 8 in 1to4

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Copper binding site 8 out of 8 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu831

b:12.2
occ:0.87
 CU D:CU831 0.0 12.2 0.9
CU D:CU831 0.9 12.2 0.1
NE2 D:HIS47 2.0 6.3 1.0
ND1 D:HIS45 2.0 7.0 1.0
NE2 D:HIS119 2.0 7.9 1.0
CD2 D:HIS47 2.9 6.5 1.0
CE1 D:HIS47 3.0 7.5 1.0
CE1 D:HIS45 3.0 8.2 1.0
CD2 D:HIS119 3.0 8.0 1.0
CG D:HIS45 3.0 7.7 1.0
CE1 D:HIS119 3.1 9.6 1.0
O D:HOH852 3.2 11.7 0.2
NE2 D:HIS62 3.3 9.1 1.0
CB D:HIS45 3.4 8.5 1.0
O D:HOH852 3.5 11.8 0.8
CD2 D:HIS62 3.7 8.7 1.0
CB D:VAL117 3.9 6.8 1.0
ND1 D:HIS47 4.1 7.5 1.0
CG D:HIS47 4.1 7.5 1.0
NE2 D:HIS45 4.1 8.8 1.0
CG1 D:VAL117 4.1 8.2 1.0
CG D:HIS119 4.1 8.6 1.0
CE1 D:HIS62 4.1 8.7 1.0
CD2 D:HIS45 4.2 9.3 1.0
ND1 D:HIS119 4.2 10.0 1.0
N D:HIS45 4.2 7.6 1.0
O D:VAL117 4.3 6.9 1.0
CA D:HIS45 4.3 6.8 1.0
O D:HIS45 4.6 6.6 1.0
CG D:HIS62 4.7 7.7 1.0
C D:HIS45 4.7 7.1 1.0
CG2 D:VAL117 4.7 7.6 1.0
C D:VAL117 4.8 6.4 1.0
ND1 D:HIS62 4.9 6.1 1.0
CA D:VAL117 4.9 6.5 1.0

Reference:

R.M.Cardoso, C.H.Silva, A.P.Ulian De Araujo, T.Tanaka, M.Tanaka, R.C.Garratt. Structure of the Cytosolic Cu,Zn Superoxide Dismutase From Schistosoma Mansoni. Acta Crystallogr.,Sect.D V. 60 1569 2004.
ISSN: ISSN 0907-4449
PubMed: 15333927
DOI: 10.1107/S0907444904016798
Page generated: Tue Jul 30 22:51:37 2024

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