Zinc in PDB 6vbt: The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution
Enzymatic activity of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution
All present enzymatic activity of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution:
1.15.1.1;
Protein crystallography data
The structure of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution, PDB code: 6vbt
was solved by
K.A.Satyshur,
K.T.Forest,
P.W.Newhouse,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.57 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.052,
57.428,
120.548,
90,
90,
90
|
R / Rfree (%)
|
17.5 /
21.2
|
Other elements in 6vbt:
The structure of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution
(pdb code 6vbt). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution, PDB code: 6vbt:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6vbt
Go back to
Zinc Binding Sites List in 6vbt
Zinc binding site 1 out
of 2 in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn202
b:10.2
occ:1.00
|
OD1
|
A:ASP95
|
1.9
|
12.2
|
1.0
|
ND1
|
A:HIS92
|
2.1
|
12.9
|
1.0
|
ND1
|
A:HIS74
|
2.1
|
14.6
|
1.0
|
ND1
|
A:HIS83
|
2.1
|
9.2
|
1.0
|
CG
|
A:ASP95
|
2.8
|
10.1
|
1.0
|
HB2
|
A:HIS92
|
2.8
|
14.5
|
1.0
|
OD2
|
A:ASP95
|
2.9
|
8.4
|
1.0
|
CE1
|
A:HIS83
|
3.0
|
9.9
|
1.0
|
CE1
|
A:HIS74
|
3.0
|
13.1
|
1.0
|
CE1
|
A:HIS92
|
3.0
|
12.6
|
1.0
|
CG
|
A:HIS92
|
3.1
|
12.5
|
1.0
|
HE1
|
A:HIS83
|
3.1
|
11.8
|
1.0
|
CG
|
A:HIS74
|
3.1
|
14.9
|
1.0
|
HA
|
A:HIS83
|
3.1
|
15.2
|
1.0
|
CG
|
A:HIS83
|
3.1
|
8.7
|
1.0
|
HE1
|
A:HIS74
|
3.2
|
15.8
|
1.0
|
HE1
|
A:HIS92
|
3.2
|
15.2
|
1.0
|
HB3
|
A:HIS74
|
3.2
|
17.7
|
1.0
|
HB2
|
A:HIS83
|
3.2
|
14.3
|
1.0
|
CB
|
A:HIS92
|
3.4
|
12.1
|
1.0
|
HB2
|
A:HIS74
|
3.4
|
17.7
|
1.0
|
CB
|
A:HIS74
|
3.5
|
14.7
|
1.0
|
CB
|
A:HIS83
|
3.5
|
11.9
|
1.0
|
HB3
|
A:HIS92
|
3.7
|
14.5
|
1.0
|
HD22
|
A:LEU143
|
3.8
|
23.9
|
1.0
|
CA
|
A:HIS83
|
3.8
|
12.7
|
1.0
|
NE2
|
A:HIS83
|
4.1
|
11.0
|
1.0
|
NE2
|
A:HIS74
|
4.1
|
16.1
|
1.0
|
NE2
|
A:HIS92
|
4.1
|
13.6
|
1.0
|
CB
|
A:ASP95
|
4.2
|
8.6
|
1.0
|
CD2
|
A:HIS92
|
4.2
|
16.3
|
1.0
|
CD2
|
A:HIS74
|
4.2
|
16.2
|
1.0
|
CD2
|
A:HIS83
|
4.2
|
8.6
|
1.0
|
HA
|
A:ASP95
|
4.3
|
12.3
|
1.0
|
H
|
A:HIS92
|
4.4
|
15.3
|
1.0
|
HB3
|
A:HIS83
|
4.5
|
14.3
|
1.0
|
HB3
|
A:ASP95
|
4.6
|
10.3
|
1.0
|
H
|
A:LEU84
|
4.6
|
13.3
|
1.0
|
HD2
|
A:HIS49
|
4.6
|
11.6
|
1.0
|
CA
|
A:ASP95
|
4.7
|
10.3
|
1.0
|
HA
|
A:LEU143
|
4.7
|
18.3
|
1.0
|
CD2
|
A:LEU143
|
4.7
|
19.9
|
1.0
|
CA
|
A:HIS92
|
4.7
|
10.7
|
1.0
|
HB2
|
A:ASP95
|
4.7
|
10.3
|
1.0
|
HB3
|
A:HIS49
|
4.8
|
12.7
|
1.0
|
HD23
|
A:LEU143
|
4.8
|
23.9
|
1.0
|
O
|
A:LYS82
|
4.8
|
14.6
|
1.0
|
CD2
|
A:HIS49
|
4.8
|
9.6
|
1.0
|
N
|
A:HIS83
|
4.8
|
13.9
|
1.0
|
H
|
A:GLY85
|
4.8
|
10.2
|
1.0
|
C
|
A:HIS83
|
4.9
|
12.1
|
1.0
|
HE2
|
A:HIS83
|
4.9
|
13.2
|
1.0
|
N
|
A:ASP95
|
4.9
|
8.6
|
1.0
|
HE2
|
A:HIS74
|
4.9
|
19.3
|
1.0
|
HE2
|
A:HIS92
|
4.9
|
16.3
|
1.0
|
H
|
A:ASP95
|
4.9
|
10.3
|
1.0
|
N
|
A:HIS92
|
4.9
|
12.8
|
1.0
|
HB3
|
A:LEU143
|
5.0
|
19.1
|
1.0
|
CA
|
A:HIS74
|
5.0
|
14.4
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6vbt
Go back to
Zinc Binding Sites List in 6vbt
Zinc binding site 2 out
of 2 in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:10.4
occ:1.00
|
OD1
|
B:ASP95
|
2.0
|
12.1
|
1.0
|
ND1
|
B:HIS83
|
2.1
|
12.8
|
1.0
|
ND1
|
B:HIS74
|
2.1
|
12.3
|
1.0
|
ND1
|
B:HIS92
|
2.1
|
10.5
|
1.0
|
CG
|
B:ASP95
|
2.7
|
12.7
|
1.0
|
HB2
|
B:HIS92
|
2.9
|
14.2
|
1.0
|
OD2
|
B:ASP95
|
2.9
|
12.5
|
1.0
|
CE1
|
B:HIS83
|
3.0
|
14.3
|
1.0
|
CE1
|
B:HIS74
|
3.0
|
13.6
|
1.0
|
HE1
|
B:HIS83
|
3.1
|
17.2
|
1.0
|
CE1
|
B:HIS92
|
3.1
|
17.7
|
1.0
|
CG
|
B:HIS74
|
3.1
|
13.5
|
1.0
|
CG
|
B:HIS92
|
3.1
|
11.3
|
1.0
|
CG
|
B:HIS83
|
3.1
|
14.0
|
1.0
|
HA
|
B:HIS83
|
3.2
|
15.4
|
1.0
|
HE1
|
B:HIS74
|
3.2
|
16.3
|
1.0
|
HB2
|
B:HIS83
|
3.2
|
13.6
|
1.0
|
HB3
|
B:HIS74
|
3.2
|
16.0
|
1.0
|
HE1
|
B:HIS92
|
3.2
|
21.3
|
1.0
|
HB2
|
B:HIS74
|
3.4
|
16.0
|
1.0
|
CB
|
B:HIS92
|
3.5
|
11.8
|
1.0
|
CB
|
B:HIS74
|
3.5
|
13.3
|
1.0
|
CB
|
B:HIS83
|
3.5
|
11.4
|
1.0
|
CA
|
B:HIS83
|
3.9
|
12.8
|
1.0
|
HD22
|
B:LEU143
|
3.9
|
22.2
|
1.0
|
HB3
|
B:HIS92
|
3.9
|
14.2
|
1.0
|
NE2
|
B:HIS83
|
4.1
|
15.4
|
1.0
|
CB
|
B:ASP95
|
4.2
|
10.8
|
1.0
|
NE2
|
B:HIS74
|
4.2
|
16.5
|
1.0
|
NE2
|
B:HIS92
|
4.2
|
13.7
|
1.0
|
CD2
|
B:HIS83
|
4.2
|
16.0
|
1.0
|
HA
|
B:ASP95
|
4.2
|
12.5
|
1.0
|
CD2
|
B:HIS74
|
4.2
|
16.4
|
1.0
|
CD2
|
B:HIS92
|
4.3
|
14.1
|
1.0
|
H
|
B:HIS92
|
4.3
|
15.0
|
1.0
|
HB3
|
B:HIS83
|
4.5
|
13.6
|
1.0
|
HD2
|
B:HIS49
|
4.5
|
13.1
|
1.0
|
HB3
|
B:ASP95
|
4.5
|
13.0
|
1.0
|
CA
|
B:ASP95
|
4.6
|
10.4
|
1.0
|
H
|
B:LEU84
|
4.6
|
18.6
|
1.0
|
CD2
|
B:HIS49
|
4.7
|
10.9
|
1.0
|
CD2
|
B:LEU143
|
4.7
|
18.5
|
1.0
|
HA
|
B:LEU143
|
4.7
|
20.6
|
1.0
|
HD23
|
B:LEU143
|
4.7
|
22.2
|
1.0
|
CA
|
B:HIS92
|
4.7
|
14.3
|
1.0
|
HB2
|
B:ASP95
|
4.7
|
13.0
|
1.0
|
O
|
B:LYS82
|
4.8
|
17.7
|
1.0
|
HB3
|
B:HIS49
|
4.8
|
12.0
|
1.0
|
N
|
B:HIS83
|
4.8
|
15.5
|
1.0
|
H
|
B:GLY85
|
4.8
|
15.2
|
1.0
|
N
|
B:ASP95
|
4.9
|
9.5
|
1.0
|
N
|
B:HIS92
|
4.9
|
12.5
|
1.0
|
C
|
B:HIS83
|
4.9
|
12.6
|
1.0
|
HE2
|
B:HIS83
|
4.9
|
18.5
|
1.0
|
H
|
B:ASP95
|
4.9
|
11.4
|
1.0
|
HE2
|
B:HIS74
|
4.9
|
19.8
|
1.0
|
HE2
|
B:HIS92
|
5.0
|
16.5
|
1.0
|
HB3
|
B:LEU143
|
5.0
|
17.4
|
1.0
|
|
Reference:
P.W.Newhouse,
K.A.Satyshur,
J.M.Slauch,
K.T.Forest.
Structure and Muropeptide Binding of the Virulence Factor Superoxide Dismutase C1 From Salmonella Typhimurium To Be Published.
Page generated: Tue Oct 29 08:58:29 2024
|