Zinc in PDB 6d52: Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
Enzymatic activity of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
All present enzymatic activity of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution:
1.15.1.1;
Protein crystallography data
The structure of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution, PDB code: 6d52
was solved by
P.W.Newhouse Ix,
K.T.Forest,
K.A.Satyshur,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
28.00 /
1.60
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.530,
68.571,
122.172,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16 /
18.4
|
Other elements in 6d52:
The structure of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
(pdb code 6d52). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution, PDB code: 6d52:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6d52
Go back to
Zinc Binding Sites List in 6d52
Zinc binding site 1 out
of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:19.8
occ:1.00
|
OD1
|
B:ASP95
|
1.9
|
17.7
|
1.0
|
|
ND1
|
B:HIS74
|
2.0
|
18.7
|
1.0
|
|
ND1
|
B:HIS92
|
2.0
|
20.1
|
1.0
|
|
ND1
|
B:HIS83
|
2.1
|
18.6
|
1.0
|
|
CG
|
B:ASP95
|
2.7
|
18.9
|
1.0
|
|
HB2
|
B:HIS92
|
2.9
|
22.1
|
1.0
|
|
OD2
|
B:ASP95
|
2.9
|
18.6
|
1.0
|
|
CE1
|
B:HIS83
|
2.9
|
17.5
|
1.0
|
|
CE1
|
B:HIS74
|
2.9
|
20.8
|
1.0
|
|
CE1
|
B:HIS92
|
3.0
|
21.1
|
1.0
|
|
HE1
|
B:HIS83
|
3.1
|
21.1
|
1.0
|
|
HE1
|
B:HIS74
|
3.1
|
25.0
|
1.0
|
|
CG
|
B:HIS92
|
3.1
|
18.7
|
1.0
|
|
CG
|
B:HIS74
|
3.1
|
20.8
|
1.0
|
|
HE1
|
B:HIS92
|
3.1
|
25.3
|
1.0
|
|
CG
|
B:HIS83
|
3.1
|
19.0
|
1.0
|
|
HA
|
B:HIS83
|
3.2
|
24.9
|
1.0
|
|
HB3
|
B:HIS74
|
3.2
|
23.8
|
1.0
|
|
HB2
|
B:HIS83
|
3.2
|
24.3
|
1.0
|
|
HB2
|
B:HIS74
|
3.4
|
23.8
|
1.0
|
|
CB
|
B:HIS92
|
3.5
|
18.4
|
1.0
|
|
CB
|
B:HIS74
|
3.5
|
19.8
|
1.0
|
|
CB
|
B:HIS83
|
3.6
|
20.2
|
1.0
|
|
HB3
|
B:HIS92
|
3.8
|
22.1
|
1.0
|
|
CA
|
B:HIS83
|
3.9
|
20.7
|
1.0
|
|
HD22
|
B:LEU143
|
4.0
|
28.5
|
1.0
|
|
NE2
|
B:HIS74
|
4.1
|
20.4
|
1.0
|
|
NE2
|
B:HIS83
|
4.1
|
17.1
|
1.0
|
|
NE2
|
B:HIS92
|
4.1
|
21.3
|
1.0
|
|
CB
|
B:ASP95
|
4.2
|
15.2
|
1.0
|
|
CD2
|
B:HIS92
|
4.2
|
22.8
|
1.0
|
|
CD2
|
B:HIS74
|
4.2
|
18.8
|
1.0
|
|
CD2
|
B:HIS83
|
4.2
|
17.6
|
1.0
|
|
HA
|
B:ASP95
|
4.3
|
20.6
|
1.0
|
|
H
|
B:HIS92
|
4.4
|
25.4
|
1.0
|
|
HD23
|
B:LEU143
|
4.5
|
28.5
|
1.0
|
|
HB3
|
B:HIS83
|
4.5
|
24.3
|
1.0
|
|
HB3
|
B:ASP95
|
4.5
|
18.2
|
1.0
|
|
HA
|
B:LEU143
|
4.6
|
25.3
|
1.0
|
|
CD2
|
B:LEU143
|
4.7
|
23.7
|
1.0
|
|
CA
|
B:ASP95
|
4.7
|
17.2
|
1.0
|
|
H
|
B:LEU84
|
4.7
|
21.3
|
1.0
|
|
HB3
|
B:HIS49
|
4.7
|
20.4
|
1.0
|
|
HB2
|
B:ASP95
|
4.7
|
18.2
|
1.0
|
|
CA
|
B:HIS92
|
4.8
|
18.6
|
1.0
|
|
HD2
|
B:HIS49
|
4.8
|
19.6
|
1.0
|
|
H
|
B:GLY85
|
4.8
|
22.9
|
1.0
|
|
CD2
|
B:HIS49
|
4.8
|
16.3
|
1.0
|
|
HE2
|
B:HIS83
|
4.9
|
20.5
|
1.0
|
|
HE2
|
B:HIS74
|
4.9
|
24.6
|
1.0
|
|
O
|
B:LYS82
|
4.9
|
21.2
|
1.0
|
|
N
|
B:HIS83
|
4.9
|
22.4
|
1.0
|
|
HE2
|
B:HIS92
|
4.9
|
25.5
|
1.0
|
|
N
|
B:ASP95
|
4.9
|
17.3
|
1.0
|
|
C
|
B:HIS83
|
4.9
|
20.0
|
1.0
|
|
H
|
B:ASP95
|
4.9
|
20.7
|
1.0
|
|
HB3
|
B:LEU143
|
4.9
|
25.2
|
1.0
|
|
N
|
B:HIS92
|
4.9
|
21.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6d52
Go back to
Zinc Binding Sites List in 6d52
Zinc binding site 2 out
of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:16.0
occ:1.00
|
ND1
|
D:HIS74
|
2.0
|
15.5
|
1.0
|
|
OD1
|
D:ASP95
|
2.0
|
15.2
|
1.0
|
|
ND1
|
D:HIS83
|
2.0
|
14.9
|
1.0
|
|
ND1
|
D:HIS92
|
2.1
|
16.7
|
1.0
|
|
CG
|
D:ASP95
|
2.8
|
15.0
|
1.0
|
|
HB2
|
D:HIS92
|
2.9
|
20.1
|
1.0
|
|
CE1
|
D:HIS74
|
2.9
|
18.2
|
1.0
|
|
CE1
|
D:HIS83
|
2.9
|
14.9
|
1.0
|
|
OD2
|
D:ASP95
|
2.9
|
15.9
|
1.0
|
|
HE1
|
D:HIS83
|
3.0
|
18.0
|
1.0
|
|
CE1
|
D:HIS92
|
3.0
|
17.2
|
1.0
|
|
HE1
|
D:HIS74
|
3.0
|
21.9
|
1.0
|
|
CG
|
D:HIS74
|
3.1
|
15.9
|
1.0
|
|
CG
|
D:HIS92
|
3.1
|
15.1
|
1.0
|
|
CG
|
D:HIS83
|
3.1
|
12.7
|
1.0
|
|
HE1
|
D:HIS92
|
3.1
|
20.7
|
1.0
|
|
HA
|
D:HIS83
|
3.2
|
17.9
|
1.0
|
|
HB3
|
D:HIS74
|
3.2
|
16.6
|
1.0
|
|
HB2
|
D:HIS83
|
3.2
|
16.7
|
1.0
|
|
HB2
|
D:HIS74
|
3.4
|
16.6
|
1.0
|
|
CB
|
D:HIS92
|
3.5
|
16.8
|
1.0
|
|
CB
|
D:HIS74
|
3.5
|
13.8
|
1.0
|
|
CB
|
D:HIS83
|
3.6
|
13.9
|
1.0
|
|
HD22
|
D:LEU143
|
3.8
|
21.5
|
1.0
|
|
HB3
|
D:HIS92
|
3.9
|
20.1
|
1.0
|
|
CA
|
D:HIS83
|
3.9
|
14.9
|
1.0
|
|
NE2
|
D:HIS74
|
4.0
|
18.0
|
1.0
|
|
NE2
|
D:HIS83
|
4.0
|
13.9
|
1.0
|
|
CD2
|
D:HIS74
|
4.1
|
18.5
|
1.0
|
|
NE2
|
D:HIS92
|
4.1
|
16.9
|
1.0
|
|
CD2
|
D:HIS83
|
4.2
|
14.7
|
1.0
|
|
CB
|
D:ASP95
|
4.2
|
13.3
|
1.0
|
|
CD2
|
D:HIS92
|
4.2
|
16.1
|
1.0
|
|
HA
|
D:ASP95
|
4.3
|
16.3
|
1.0
|
|
H
|
D:HIS92
|
4.3
|
17.5
|
1.0
|
|
HD23
|
D:LEU143
|
4.4
|
21.5
|
1.0
|
|
HB3
|
D:HIS83
|
4.5
|
16.7
|
1.0
|
|
CD2
|
D:LEU143
|
4.6
|
17.9
|
1.0
|
|
HB3
|
D:ASP95
|
4.6
|
16.0
|
1.0
|
|
HA
|
D:LEU143
|
4.6
|
19.4
|
1.0
|
|
H
|
D:LEU84
|
4.7
|
15.8
|
1.0
|
|
CA
|
D:ASP95
|
4.7
|
13.6
|
1.0
|
|
HB3
|
D:HIS49
|
4.7
|
18.4
|
1.0
|
|
HD2
|
D:HIS49
|
4.7
|
15.1
|
1.0
|
|
CA
|
D:HIS92
|
4.7
|
14.9
|
1.0
|
|
CD2
|
D:HIS49
|
4.8
|
12.6
|
1.0
|
|
HB2
|
D:ASP95
|
4.8
|
16.0
|
1.0
|
|
HE2
|
D:HIS74
|
4.8
|
21.6
|
1.0
|
|
HE2
|
D:HIS83
|
4.8
|
16.8
|
1.0
|
|
O
|
D:LYS82
|
4.8
|
15.9
|
1.0
|
|
H
|
D:GLY85
|
4.8
|
17.7
|
1.0
|
|
N
|
D:HIS83
|
4.9
|
15.9
|
1.0
|
|
N
|
D:HIS92
|
4.9
|
14.6
|
1.0
|
|
N
|
D:ASP95
|
4.9
|
14.7
|
1.0
|
|
H
|
D:ASP95
|
4.9
|
17.7
|
1.0
|
|
C
|
D:HIS83
|
4.9
|
16.0
|
1.0
|
|
HE2
|
D:HIS92
|
4.9
|
20.3
|
1.0
|
|
CA
|
D:HIS74
|
5.0
|
15.2
|
1.0
|
|
CG
|
D:HIS49
|
5.0
|
12.9
|
1.0
|
|
HD2
|
D:HIS74
|
5.0
|
22.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6d52
Go back to
Zinc Binding Sites List in 6d52
Zinc binding site 3 out
of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:18.5
occ:1.00
|
OD1
|
C:ASP95
|
2.0
|
17.0
|
1.0
|
|
ND1
|
C:HIS83
|
2.0
|
18.5
|
1.0
|
|
ND1
|
C:HIS74
|
2.0
|
22.2
|
1.0
|
|
ND1
|
C:HIS92
|
2.1
|
16.5
|
1.0
|
|
CG
|
C:ASP95
|
2.8
|
16.1
|
1.0
|
|
HB2
|
C:HIS92
|
2.8
|
23.3
|
1.0
|
|
CE1
|
C:HIS83
|
2.9
|
19.4
|
1.0
|
|
OD2
|
C:ASP95
|
2.9
|
16.2
|
1.0
|
|
CE1
|
C:HIS74
|
3.0
|
18.4
|
1.0
|
|
HE1
|
C:HIS83
|
3.0
|
23.3
|
1.0
|
|
CG
|
C:HIS74
|
3.1
|
19.0
|
1.0
|
|
CE1
|
C:HIS92
|
3.1
|
18.5
|
1.0
|
|
CG
|
C:HIS83
|
3.1
|
22.2
|
1.0
|
|
HE1
|
C:HIS74
|
3.1
|
22.1
|
1.0
|
|
CG
|
C:HIS92
|
3.1
|
17.2
|
1.0
|
|
HA
|
C:HIS83
|
3.2
|
21.4
|
1.0
|
|
HB2
|
C:HIS83
|
3.2
|
22.1
|
1.0
|
|
HB3
|
C:HIS74
|
3.2
|
21.9
|
1.0
|
|
HE1
|
C:HIS92
|
3.3
|
22.3
|
1.0
|
|
HB2
|
C:HIS74
|
3.4
|
21.9
|
1.0
|
|
CB
|
C:HIS92
|
3.4
|
19.4
|
1.0
|
|
CB
|
C:HIS74
|
3.5
|
18.2
|
1.0
|
|
CB
|
C:HIS83
|
3.5
|
18.4
|
1.0
|
|
HB3
|
C:HIS92
|
3.7
|
23.3
|
1.0
|
|
CA
|
C:HIS83
|
3.8
|
17.8
|
1.0
|
|
HD22
|
C:LEU143
|
4.0
|
27.9
|
1.0
|
|
NE2
|
C:HIS83
|
4.1
|
17.4
|
1.0
|
|
NE2
|
C:HIS74
|
4.1
|
21.9
|
1.0
|
|
CB
|
C:ASP95
|
4.2
|
15.2
|
1.0
|
|
CD2
|
C:HIS83
|
4.2
|
17.8
|
1.0
|
|
CD2
|
C:HIS74
|
4.2
|
22.6
|
1.0
|
|
NE2
|
C:HIS92
|
4.2
|
19.4
|
1.0
|
|
CD2
|
C:HIS92
|
4.3
|
20.1
|
1.0
|
|
HA
|
C:ASP95
|
4.3
|
17.7
|
1.0
|
|
H
|
C:HIS92
|
4.4
|
22.9
|
1.0
|
|
HB3
|
C:HIS83
|
4.5
|
22.1
|
1.0
|
|
HB3
|
C:ASP95
|
4.6
|
18.3
|
1.0
|
|
CA
|
C:ASP95
|
4.7
|
14.8
|
1.0
|
|
HA
|
C:LEU143
|
4.7
|
25.1
|
1.0
|
|
HB3
|
C:HIS49
|
4.7
|
22.2
|
1.0
|
|
H
|
C:LEU84
|
4.7
|
24.3
|
1.0
|
|
HD23
|
C:LEU143
|
4.7
|
27.9
|
1.0
|
|
HD2
|
C:HIS49
|
4.7
|
21.3
|
1.0
|
|
CA
|
C:HIS92
|
4.8
|
18.5
|
1.0
|
|
CD2
|
C:HIS49
|
4.8
|
17.7
|
1.0
|
|
HB2
|
C:ASP95
|
4.8
|
18.3
|
1.0
|
|
O
|
C:LYS82
|
4.8
|
19.4
|
1.0
|
|
CD2
|
C:LEU143
|
4.8
|
23.2
|
1.0
|
|
N
|
C:HIS83
|
4.8
|
19.1
|
1.0
|
|
H
|
C:GLY85
|
4.8
|
21.2
|
1.0
|
|
HE2
|
C:HIS83
|
4.8
|
20.9
|
1.0
|
|
N
|
C:ASP95
|
4.9
|
16.3
|
1.0
|
|
C
|
C:HIS83
|
4.9
|
20.8
|
1.0
|
|
HE2
|
C:HIS74
|
4.9
|
26.3
|
1.0
|
|
H
|
C:ASP95
|
4.9
|
19.6
|
1.0
|
|
CG
|
C:HIS49
|
5.0
|
16.4
|
1.0
|
|
HB3
|
C:LEU143
|
5.0
|
23.4
|
1.0
|
|
N
|
C:HIS92
|
5.0
|
19.1
|
1.0
|
|
CA
|
C:HIS74
|
5.0
|
18.8
|
1.0
|
|
HE2
|
C:HIS92
|
5.0
|
23.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6d52
Go back to
Zinc Binding Sites List in 6d52
Zinc binding site 4 out
of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:15.4
occ:1.00
|
OD1
|
A:ASP95
|
1.9
|
15.4
|
1.0
|
|
ND1
|
A:HIS74
|
2.0
|
16.9
|
1.0
|
|
ND1
|
A:HIS92
|
2.1
|
15.0
|
1.0
|
|
ND1
|
A:HIS83
|
2.1
|
17.0
|
1.0
|
|
CG
|
A:ASP95
|
2.8
|
15.7
|
1.0
|
|
HB2
|
A:HIS92
|
2.9
|
19.6
|
1.0
|
|
OD2
|
A:ASP95
|
2.9
|
14.8
|
1.0
|
|
CE1
|
A:HIS74
|
2.9
|
17.0
|
1.0
|
|
CE1
|
A:HIS83
|
3.0
|
15.7
|
1.0
|
|
CE1
|
A:HIS92
|
3.0
|
19.2
|
1.0
|
|
CG
|
A:HIS74
|
3.1
|
14.7
|
1.0
|
|
HE1
|
A:HIS74
|
3.1
|
20.4
|
1.0
|
|
HE1
|
A:HIS83
|
3.1
|
18.8
|
1.0
|
|
CG
|
A:HIS92
|
3.1
|
14.8
|
1.0
|
|
CG
|
A:HIS83
|
3.1
|
17.2
|
1.0
|
|
HE1
|
A:HIS92
|
3.2
|
23.1
|
1.0
|
|
HA
|
A:HIS83
|
3.2
|
20.3
|
1.0
|
|
HB2
|
A:HIS83
|
3.2
|
19.2
|
1.0
|
|
HB3
|
A:HIS74
|
3.2
|
19.8
|
1.0
|
|
HB2
|
A:HIS74
|
3.4
|
19.8
|
1.0
|
|
CB
|
A:HIS92
|
3.4
|
16.3
|
1.0
|
|
CB
|
A:HIS74
|
3.5
|
16.5
|
1.0
|
|
CB
|
A:HIS83
|
3.5
|
16.0
|
1.0
|
|
HB3
|
A:HIS92
|
3.8
|
19.6
|
1.0
|
|
CA
|
A:HIS83
|
3.8
|
16.9
|
1.0
|
|
HD22
|
A:LEU143
|
3.9
|
21.7
|
1.0
|
|
NE2
|
A:HIS74
|
4.1
|
18.6
|
1.0
|
|
NE2
|
A:HIS83
|
4.1
|
14.6
|
1.0
|
|
NE2
|
A:HIS92
|
4.1
|
17.2
|
1.0
|
|
CD2
|
A:HIS74
|
4.2
|
17.2
|
1.0
|
|
CB
|
A:ASP95
|
4.2
|
15.2
|
1.0
|
|
CD2
|
A:HIS92
|
4.2
|
16.8
|
1.0
|
|
CD2
|
A:HIS83
|
4.2
|
14.2
|
1.0
|
|
HA
|
A:ASP95
|
4.3
|
17.5
|
1.0
|
|
H
|
A:HIS92
|
4.4
|
18.7
|
1.0
|
|
HB3
|
A:HIS83
|
4.5
|
19.2
|
1.0
|
|
HB3
|
A:ASP95
|
4.6
|
18.2
|
1.0
|
|
HB3
|
A:HIS49
|
4.6
|
18.4
|
1.0
|
|
H
|
A:LEU84
|
4.7
|
20.7
|
1.0
|
|
CA
|
A:ASP95
|
4.7
|
14.6
|
1.0
|
|
HA
|
A:LEU143
|
4.7
|
18.4
|
1.0
|
|
HD2
|
A:HIS49
|
4.7
|
17.3
|
1.0
|
|
HB2
|
A:ASP95
|
4.8
|
18.2
|
1.0
|
|
O
|
A:LYS82
|
4.8
|
17.8
|
1.0
|
|
N
|
A:HIS83
|
4.8
|
16.8
|
1.0
|
|
CD2
|
A:LEU143
|
4.8
|
18.1
|
1.0
|
|
HD23
|
A:LEU143
|
4.8
|
21.7
|
1.0
|
|
CD2
|
A:HIS49
|
4.8
|
14.4
|
1.0
|
|
CA
|
A:HIS92
|
4.8
|
15.5
|
1.0
|
|
H
|
A:GLY85
|
4.8
|
20.7
|
1.0
|
|
HE2
|
A:HIS74
|
4.8
|
22.4
|
1.0
|
|
C
|
A:HIS83
|
4.9
|
17.2
|
1.0
|
|
N
|
A:ASP95
|
4.9
|
13.4
|
1.0
|
|
HE2
|
A:HIS83
|
4.9
|
17.6
|
1.0
|
|
H
|
A:ASP95
|
4.9
|
16.1
|
1.0
|
|
HE2
|
A:HIS92
|
4.9
|
20.7
|
1.0
|
|
CG
|
A:HIS49
|
5.0
|
12.8
|
1.0
|
|
CA
|
A:HIS74
|
5.0
|
14.2
|
1.0
|
|
Reference:
P.W.Newhouse Ix,
K.A.Satyshur,
K.T.Forest,
J.M.Slauch.
Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution To Be Published.
Page generated: Wed Dec 16 11:39:03 2020
|
