Copper in PDB 2sod: Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
Enzymatic activity of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
All present enzymatic activity of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase:
1.15.1.1;
Protein crystallography data
The structure of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase, PDB code: 2sod
was solved by
J.A.Tainer,
E.D.Getzoff,
J.S.Richardson,
D.C.Richardson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.650,
90.330,
71.650,
90.00,
95.10,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 2sod:
The structure of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
(pdb code 2sod). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase, PDB code: 2sod:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 2sod
Go back to
Copper Binding Sites List in 2sod
Copper binding site 1 out
of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cu152
b:10.9
occ:1.00
|
ND1
|
O:HIS44
|
2.0
|
10.6
|
1.0
|
NE2
|
O:HIS118
|
2.1
|
5.9
|
1.0
|
NE2
|
O:HIS46
|
2.1
|
10.5
|
1.0
|
NE2
|
O:HIS61
|
2.2
|
9.5
|
1.0
|
CE1
|
O:HIS46
|
2.9
|
9.6
|
1.0
|
CG
|
O:HIS44
|
2.9
|
9.9
|
1.0
|
CE1
|
O:HIS118
|
3.0
|
5.2
|
1.0
|
CE1
|
O:HIS44
|
3.0
|
10.8
|
1.0
|
CD2
|
O:HIS118
|
3.1
|
5.0
|
1.0
|
CD2
|
O:HIS61
|
3.1
|
10.0
|
1.0
|
CB
|
O:HIS44
|
3.2
|
10.4
|
1.0
|
O
|
O:HOH154
|
3.2
|
11.0
|
1.0
|
CD2
|
O:HIS46
|
3.2
|
8.1
|
1.0
|
CE1
|
O:HIS61
|
3.3
|
9.3
|
1.0
|
CG1
|
O:VAL116
|
4.0
|
11.6
|
1.0
|
ND1
|
O:HIS118
|
4.0
|
4.1
|
1.0
|
CD2
|
O:HIS44
|
4.1
|
9.7
|
1.0
|
NE2
|
O:HIS44
|
4.1
|
8.7
|
1.0
|
CG
|
O:HIS118
|
4.1
|
6.0
|
1.0
|
ND1
|
O:HIS46
|
4.1
|
7.8
|
1.0
|
CG
|
O:HIS61
|
4.3
|
10.6
|
1.0
|
CG
|
O:HIS46
|
4.3
|
8.0
|
1.0
|
ND1
|
O:HIS61
|
4.3
|
10.4
|
1.0
|
CA
|
O:HIS44
|
4.8
|
11.8
|
1.0
|
|
Copper binding site 2 out
of 4 in 2sod
Go back to
Copper Binding Sites List in 2sod
Copper binding site 2 out
of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Cu152
b:11.3
occ:1.00
|
ND1
|
Y:HIS44
|
2.0
|
9.2
|
1.0
|
NE2
|
Y:HIS61
|
2.0
|
9.2
|
1.0
|
NE2
|
Y:HIS118
|
2.0
|
9.3
|
1.0
|
NE2
|
Y:HIS46
|
2.1
|
11.1
|
1.0
|
O
|
Y:HOH154
|
2.5
|
11.1
|
1.0
|
CE1
|
Y:HIS118
|
2.9
|
7.6
|
1.0
|
CE1
|
Y:HIS61
|
2.9
|
9.5
|
1.0
|
CG
|
Y:HIS44
|
3.0
|
10.3
|
1.0
|
CE1
|
Y:HIS44
|
3.0
|
8.5
|
1.0
|
CE1
|
Y:HIS46
|
3.0
|
9.4
|
1.0
|
CD2
|
Y:HIS118
|
3.0
|
9.2
|
1.0
|
CD2
|
Y:HIS61
|
3.0
|
8.8
|
1.0
|
CD2
|
Y:HIS46
|
3.2
|
10.1
|
1.0
|
CB
|
Y:HIS44
|
3.3
|
9.9
|
1.0
|
CG1
|
Y:VAL116
|
3.8
|
11.9
|
1.0
|
ND1
|
Y:HIS118
|
4.0
|
6.5
|
1.0
|
NE2
|
Y:HIS44
|
4.0
|
7.4
|
1.0
|
CD2
|
Y:HIS44
|
4.1
|
8.6
|
1.0
|
ND1
|
Y:HIS61
|
4.1
|
10.6
|
1.0
|
CG
|
Y:HIS118
|
4.1
|
9.3
|
1.0
|
ND1
|
Y:HIS46
|
4.1
|
9.6
|
1.0
|
CG
|
Y:HIS61
|
4.1
|
10.6
|
1.0
|
CG
|
Y:HIS46
|
4.3
|
9.2
|
1.0
|
CA
|
Y:HIS44
|
4.7
|
11.8
|
1.0
|
O
|
Y:THR135
|
4.8
|
13.6
|
1.0
|
N
|
Y:HIS44
|
5.0
|
11.8
|
1.0
|
O
|
Y:HIS44
|
5.0
|
11.8
|
1.0
|
|
Copper binding site 3 out
of 4 in 2sod
Go back to
Copper Binding Sites List in 2sod
Copper binding site 3 out
of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu152
b:11.2
occ:1.00
|
NE2
|
B:HIS118
|
2.0
|
7.2
|
1.0
|
ND1
|
B:HIS44
|
2.0
|
10.2
|
1.0
|
NE2
|
B:HIS46
|
2.1
|
6.2
|
1.0
|
NE2
|
B:HIS61
|
2.3
|
8.3
|
1.0
|
CE1
|
B:HIS44
|
2.9
|
8.7
|
1.0
|
CE1
|
B:HIS118
|
2.9
|
6.2
|
1.0
|
CD2
|
B:HIS118
|
3.0
|
7.8
|
1.0
|
CE1
|
B:HIS46
|
3.0
|
5.8
|
1.0
|
CG
|
B:HIS44
|
3.0
|
10.3
|
1.0
|
CD2
|
B:HIS61
|
3.1
|
7.4
|
1.0
|
CD2
|
B:HIS46
|
3.2
|
5.5
|
1.0
|
CE1
|
B:HIS61
|
3.3
|
7.2
|
1.0
|
CB
|
B:HIS44
|
3.5
|
10.4
|
1.0
|
O
|
B:HOH154
|
3.9
|
8.5
|
1.0
|
CG1
|
B:VAL116
|
4.0
|
10.8
|
1.0
|
ND1
|
B:HIS118
|
4.0
|
7.0
|
1.0
|
NE2
|
B:HIS44
|
4.0
|
8.8
|
1.0
|
CG
|
B:HIS118
|
4.1
|
7.7
|
1.0
|
CD2
|
B:HIS44
|
4.1
|
9.0
|
1.0
|
ND1
|
B:HIS46
|
4.2
|
5.1
|
1.0
|
CG
|
B:HIS61
|
4.2
|
9.3
|
1.0
|
ND1
|
B:HIS61
|
4.3
|
9.1
|
1.0
|
CG
|
B:HIS46
|
4.3
|
6.6
|
1.0
|
CA
|
B:HIS44
|
4.6
|
11.9
|
1.0
|
N
|
B:HIS44
|
4.6
|
11.8
|
1.0
|
CB
|
B:VAL116
|
4.8
|
10.2
|
1.0
|
C
|
B:HIS44
|
4.9
|
11.9
|
1.0
|
O
|
B:HIS44
|
5.0
|
11.7
|
1.0
|
|
Copper binding site 4 out
of 4 in 2sod
Go back to
Copper Binding Sites List in 2sod
Copper binding site 4 out
of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cu152
b:11.7
occ:1.00
|
NE2
|
G:HIS46
|
2.0
|
8.8
|
1.0
|
ND1
|
G:HIS44
|
2.1
|
9.5
|
1.0
|
NE2
|
G:HIS118
|
2.1
|
9.4
|
1.0
|
NE2
|
G:HIS61
|
2.2
|
9.6
|
1.0
|
CG
|
G:HIS44
|
2.9
|
9.2
|
1.0
|
CE1
|
G:HIS46
|
2.9
|
8.2
|
1.0
|
CD2
|
G:HIS61
|
3.0
|
10.0
|
1.0
|
CE1
|
G:HIS44
|
3.0
|
9.0
|
1.0
|
CD2
|
G:HIS46
|
3.0
|
9.0
|
1.0
|
CE1
|
G:HIS118
|
3.0
|
8.7
|
1.0
|
CD2
|
G:HIS118
|
3.1
|
9.2
|
1.0
|
CB
|
G:HIS44
|
3.2
|
10.4
|
1.0
|
CE1
|
G:HIS61
|
3.3
|
9.1
|
1.0
|
O
|
G:HOH154
|
3.8
|
16.0
|
1.0
|
CD2
|
G:HIS44
|
3.9
|
8.5
|
1.0
|
NE2
|
G:HIS44
|
3.9
|
8.8
|
1.0
|
ND1
|
G:HIS46
|
4.0
|
8.2
|
1.0
|
CG
|
G:HIS46
|
4.1
|
8.5
|
1.0
|
ND1
|
G:HIS118
|
4.1
|
7.2
|
1.0
|
CG
|
G:HIS118
|
4.2
|
9.1
|
1.0
|
CG
|
G:HIS61
|
4.2
|
10.1
|
1.0
|
ND1
|
G:HIS61
|
4.3
|
9.0
|
1.0
|
CA
|
G:HIS44
|
4.5
|
11.8
|
1.0
|
CG1
|
G:VAL116
|
4.6
|
8.3
|
1.0
|
N
|
G:HIS44
|
4.7
|
11.8
|
1.0
|
CG2
|
G:VAL116
|
4.8
|
8.9
|
1.0
|
C
|
G:HIS44
|
5.0
|
11.9
|
1.0
|
|
Reference:
J.A.Tainer,
E.D.Getzoff,
K.M.Beem,
J.S.Richardson,
D.C.Richardson.
Determination and Analysis of the 2 A-Structure of Copper, Zinc Superoxide Dismutase. J.Mol.Biol. V. 160 181 1982.
ISSN: ISSN 0022-2836
PubMed: 7175933
DOI: 10.1016/0022-2836(82)90174-7
Page generated: Wed Jul 31 00:01:49 2024
|