Copper in PDB 1sda: Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
Enzymatic activity of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
All present enzymatic activity of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase:
1.15.1.1;
Protein crystallography data
The structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase, PDB code: 1sda
was solved by
C.D.Smith,
M.Carson,
M.Van Der Woerd,
J.Chen,
H.Ischiropoulos,
J.S.Beckman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.50
|
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 (%)
|
18.7 /
n/a
|
Other elements in 1sda:
The structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
(pdb code 1sda). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase, PDB code: 1sda:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 1sda
Go back to
Copper Binding Sites List in 1sda
Copper binding site 1 out
of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cu801
b:17.9
occ:1.00
|
ND1
|
O:HIS44
|
2.0
|
5.3
|
1.0
|
NE2
|
O:HIS118
|
2.1
|
7.1
|
1.0
|
NE2
|
O:HIS46
|
2.2
|
10.1
|
1.0
|
NE2
|
O:HIS61
|
2.4
|
2.0
|
1.0
|
CG
|
O:HIS44
|
2.6
|
6.0
|
1.0
|
CB
|
O:HIS44
|
2.7
|
6.1
|
1.0
|
CD2
|
O:HIS118
|
2.9
|
9.1
|
1.0
|
CD2
|
O:HIS61
|
3.1
|
2.0
|
1.0
|
CE1
|
O:HIS46
|
3.1
|
9.6
|
1.0
|
CE1
|
O:HIS44
|
3.1
|
3.4
|
1.0
|
CD2
|
O:HIS46
|
3.2
|
7.8
|
1.0
|
CE1
|
O:HIS118
|
3.2
|
7.6
|
1.0
|
CE1
|
O:HIS61
|
3.4
|
3.8
|
1.0
|
CD2
|
O:HIS44
|
3.9
|
5.5
|
1.0
|
CG
|
O:HIS118
|
4.1
|
7.5
|
1.0
|
NE2
|
O:HIS44
|
4.1
|
6.3
|
1.0
|
CA
|
O:HIS44
|
4.1
|
6.1
|
1.0
|
ND1
|
O:HIS118
|
4.2
|
6.7
|
1.0
|
ND1
|
O:HIS46
|
4.2
|
8.1
|
1.0
|
CG
|
O:HIS61
|
4.3
|
2.7
|
1.0
|
CG
|
O:HIS46
|
4.3
|
8.3
|
1.0
|
ND1
|
O:HIS61
|
4.4
|
3.1
|
1.0
|
N
|
O:HIS44
|
4.5
|
7.6
|
1.0
|
CB
|
O:VAL116
|
4.7
|
7.4
|
1.0
|
C
|
O:HIS44
|
4.8
|
4.6
|
1.0
|
O
|
O:HIS44
|
4.8
|
3.3
|
1.0
|
O
|
O:HOH803
|
4.9
|
19.6
|
1.0
|
|
Copper binding site 2 out
of 4 in 1sda
Go back to
Copper Binding Sites List in 1sda
Copper binding site 2 out
of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Cu804
b:20.2
occ:1.00
|
ND1
|
Y:HIS44
|
1.8
|
9.7
|
1.0
|
NE2
|
Y:HIS118
|
2.0
|
9.8
|
1.0
|
NE2
|
Y:HIS61
|
2.1
|
6.6
|
1.0
|
NE2
|
Y:HIS46
|
2.3
|
6.3
|
1.0
|
CG
|
Y:HIS44
|
2.7
|
8.8
|
1.0
|
CD2
|
Y:HIS61
|
2.8
|
4.2
|
1.0
|
CE1
|
Y:HIS118
|
2.8
|
10.0
|
1.0
|
CE1
|
Y:HIS44
|
2.9
|
9.9
|
1.0
|
CD2
|
Y:HIS118
|
3.0
|
9.6
|
1.0
|
CB
|
Y:HIS44
|
3.0
|
7.5
|
1.0
|
CE1
|
Y:HIS46
|
3.1
|
3.8
|
1.0
|
CE1
|
Y:HIS61
|
3.2
|
6.4
|
1.0
|
CD2
|
Y:HIS46
|
3.3
|
3.6
|
1.0
|
CD2
|
Y:HIS44
|
3.9
|
8.9
|
1.0
|
NE2
|
Y:HIS44
|
3.9
|
9.3
|
1.0
|
ND1
|
Y:HIS118
|
4.0
|
9.9
|
1.0
|
CG
|
Y:HIS61
|
4.0
|
4.9
|
1.0
|
CG
|
Y:HIS118
|
4.1
|
10.9
|
1.0
|
ND1
|
Y:HIS61
|
4.2
|
8.8
|
1.0
|
ND1
|
Y:HIS46
|
4.3
|
4.2
|
1.0
|
CA
|
Y:HIS44
|
4.4
|
6.9
|
1.0
|
CG
|
Y:HIS46
|
4.4
|
3.5
|
1.0
|
N
|
Y:HIS44
|
4.6
|
7.6
|
1.0
|
O
|
Y:HOH806
|
4.7
|
17.8
|
1.0
|
CG1
|
Y:VAL116
|
4.9
|
8.9
|
1.0
|
O
|
Y:THR135
|
4.9
|
14.7
|
1.0
|
O
|
Y:HIS44
|
5.0
|
9.2
|
1.0
|
C
|
Y:HIS44
|
5.0
|
7.4
|
1.0
|
CB
|
Y:VAL116
|
5.0
|
8.7
|
1.0
|
|
Copper binding site 3 out
of 4 in 1sda
Go back to
Copper Binding Sites List in 1sda
Copper binding site 3 out
of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu807
b:13.4
occ:1.00
|
ND1
|
B:HIS44
|
1.9
|
7.4
|
1.0
|
NE2
|
B:HIS118
|
2.0
|
9.5
|
1.0
|
NE2
|
B:HIS46
|
2.1
|
5.9
|
1.0
|
NE2
|
B:HIS61
|
2.3
|
9.8
|
1.0
|
CG
|
B:HIS44
|
2.8
|
8.2
|
1.0
|
CE1
|
B:HIS46
|
2.8
|
6.7
|
1.0
|
CD2
|
B:HIS61
|
2.8
|
8.6
|
1.0
|
CE1
|
B:HIS118
|
2.9
|
9.0
|
1.0
|
CD2
|
B:HIS118
|
3.0
|
9.8
|
1.0
|
CE1
|
B:HIS44
|
3.0
|
9.8
|
1.0
|
CB
|
B:HIS44
|
3.1
|
7.6
|
1.0
|
CD2
|
B:HIS46
|
3.2
|
5.2
|
1.0
|
CE1
|
B:HIS61
|
3.4
|
9.9
|
1.0
|
CD2
|
B:HIS44
|
3.9
|
7.9
|
1.0
|
ND1
|
B:HIS46
|
4.0
|
7.4
|
1.0
|
NE2
|
B:HIS44
|
4.0
|
7.2
|
1.0
|
ND1
|
B:HIS118
|
4.1
|
10.6
|
1.0
|
CG
|
B:HIS118
|
4.1
|
10.1
|
1.0
|
CG
|
B:HIS61
|
4.1
|
8.1
|
1.0
|
CG
|
B:HIS46
|
4.2
|
6.1
|
1.0
|
ND1
|
B:HIS61
|
4.4
|
9.1
|
1.0
|
CA
|
B:HIS44
|
4.5
|
4.8
|
1.0
|
O
|
B:HOH809
|
4.6
|
12.5
|
1.0
|
CG1
|
B:VAL116
|
4.6
|
5.0
|
1.0
|
N
|
B:HIS44
|
4.8
|
6.6
|
1.0
|
CB
|
B:VAL116
|
4.8
|
6.1
|
1.0
|
|
Copper binding site 4 out
of 4 in 1sda
Go back to
Copper Binding Sites List in 1sda
Copper binding site 4 out
of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cu810
b:21.7
occ:1.00
|
ND1
|
G:HIS44
|
1.8
|
11.7
|
1.0
|
NE2
|
G:HIS46
|
2.1
|
7.1
|
1.0
|
NE2
|
G:HIS118
|
2.1
|
9.4
|
1.0
|
NE2
|
G:HIS61
|
2.2
|
14.2
|
1.0
|
CD2
|
G:HIS61
|
2.7
|
13.3
|
1.0
|
CE1
|
G:HIS44
|
2.7
|
10.1
|
1.0
|
CG
|
G:HIS44
|
2.8
|
10.0
|
1.0
|
CE1
|
G:HIS118
|
2.9
|
9.1
|
1.0
|
CE1
|
G:HIS46
|
3.0
|
6.3
|
1.0
|
CD2
|
G:HIS46
|
3.1
|
5.5
|
1.0
|
CB
|
G:HIS44
|
3.2
|
8.9
|
1.0
|
CD2
|
G:HIS118
|
3.2
|
9.6
|
1.0
|
CE1
|
G:HIS61
|
3.4
|
14.5
|
1.0
|
NE2
|
G:HIS44
|
3.8
|
10.1
|
1.0
|
CD2
|
G:HIS44
|
3.8
|
8.7
|
1.0
|
CG
|
G:HIS61
|
3.9
|
11.8
|
1.0
|
ND1
|
G:HIS118
|
4.1
|
6.8
|
1.0
|
ND1
|
G:HIS46
|
4.2
|
6.4
|
1.0
|
CG
|
G:HIS46
|
4.2
|
5.5
|
1.0
|
ND1
|
G:HIS61
|
4.2
|
14.4
|
1.0
|
CG
|
G:HIS118
|
4.3
|
10.0
|
1.0
|
CA
|
G:HIS44
|
4.4
|
10.0
|
1.0
|
N
|
G:HIS44
|
4.6
|
10.3
|
1.0
|
CB
|
G:VAL116
|
4.7
|
4.1
|
1.0
|
CG1
|
G:VAL116
|
4.9
|
2.8
|
1.0
|
C
|
G:HIS44
|
5.0
|
9.5
|
1.0
|
|
Reference:
C.D.Smith,
M.Carson,
M.Van Der Woerd,
J.Chen,
H.Ischiropoulos,
J.S.Beckman.
Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase. Arch.Biochem.Biophys. V. 299 350 1992.
ISSN: ISSN 0003-9861
PubMed: 1444476
DOI: 10.1016/0003-9861(92)90286-6
Page generated: Tue Jul 30 22:43:50 2024
|