Zinc in PDB 1z9n: X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
Enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
All present enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface:
1.15.1.1;
Protein crystallography data
The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface, PDB code: 1z9n
was solved by
K.Djinovic Carugo,
I.Toeroe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.50 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.320,
65.900,
69.540,
66.59,
89.87,
76.03
|
R / Rfree (%)
|
15.7 /
19.3
|
Other elements in 1z9n:
The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
(pdb code 1z9n). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface, PDB code: 1z9n:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1z9n
Go back to
Zinc Binding Sites List in 1z9n
Zinc binding site 1 out
of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:12.0
occ:1.00
|
OD1
|
A:ASP116
|
2.0
|
10.7
|
1.0
|
ND1
|
A:HIS95
|
2.1
|
12.2
|
1.0
|
ND1
|
A:HIS113
|
2.1
|
11.5
|
1.0
|
ND1
|
A:HIS104
|
2.1
|
10.0
|
1.0
|
CG
|
A:ASP116
|
2.7
|
11.1
|
1.0
|
OD2
|
A:ASP116
|
2.8
|
11.6
|
1.0
|
CE1
|
A:HIS104
|
2.9
|
10.0
|
1.0
|
CE1
|
A:HIS113
|
3.0
|
14.0
|
1.0
|
CE1
|
A:HIS95
|
3.0
|
12.2
|
1.0
|
CG
|
A:HIS95
|
3.1
|
12.8
|
1.0
|
CG
|
A:HIS113
|
3.1
|
12.3
|
1.0
|
CG
|
A:HIS104
|
3.2
|
10.3
|
1.0
|
CB
|
A:HIS95
|
3.5
|
14.4
|
1.0
|
CB
|
A:HIS113
|
3.5
|
10.7
|
1.0
|
CB
|
A:HIS104
|
3.6
|
10.4
|
1.0
|
CA
|
A:HIS104
|
3.8
|
12.6
|
1.0
|
NE2
|
A:HIS104
|
4.1
|
10.6
|
1.0
|
NE2
|
A:HIS113
|
4.1
|
14.1
|
1.0
|
NE2
|
A:HIS95
|
4.1
|
14.3
|
1.0
|
CB
|
A:ASP116
|
4.2
|
9.8
|
1.0
|
CD2
|
A:HIS95
|
4.2
|
14.9
|
1.0
|
CD2
|
A:HIS113
|
4.2
|
14.2
|
1.0
|
CD2
|
A:HIS104
|
4.3
|
11.0
|
1.0
|
CD2
|
A:LEU164
|
4.4
|
15.2
|
1.0
|
CA
|
A:ASP116
|
4.7
|
9.9
|
1.0
|
N
|
A:GLY105
|
4.7
|
12.4
|
1.0
|
CA
|
A:HIS113
|
4.8
|
12.8
|
1.0
|
N
|
A:HIS104
|
4.8
|
12.4
|
1.0
|
C
|
A:HIS104
|
4.8
|
13.2
|
1.0
|
CD2
|
A:HIS70
|
4.8
|
11.4
|
1.0
|
N
|
A:HIS113
|
4.8
|
13.4
|
1.0
|
N
|
A:ASP116
|
4.8
|
11.0
|
1.0
|
CG
|
A:HIS70
|
4.9
|
11.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1z9n
Go back to
Zinc Binding Sites List in 1z9n
Zinc binding site 2 out
of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:10.8
occ:1.00
|
OD1
|
B:ASP116
|
2.0
|
9.2
|
1.0
|
ND1
|
B:HIS104
|
2.0
|
9.9
|
1.0
|
ND1
|
B:HIS113
|
2.1
|
11.1
|
1.0
|
ND1
|
B:HIS95
|
2.1
|
11.8
|
1.0
|
CG
|
B:ASP116
|
2.7
|
8.1
|
1.0
|
OD2
|
B:ASP116
|
2.8
|
10.7
|
1.0
|
CE1
|
B:HIS104
|
2.9
|
9.8
|
1.0
|
CE1
|
B:HIS95
|
3.0
|
16.8
|
1.0
|
CE1
|
B:HIS113
|
3.0
|
12.1
|
1.0
|
CG
|
B:HIS113
|
3.1
|
11.8
|
1.0
|
CG
|
B:HIS95
|
3.1
|
11.8
|
1.0
|
CG
|
B:HIS104
|
3.2
|
10.7
|
1.0
|
CB
|
B:HIS113
|
3.5
|
11.3
|
1.0
|
CB
|
B:HIS95
|
3.5
|
12.1
|
1.0
|
CB
|
B:HIS104
|
3.6
|
11.2
|
1.0
|
CA
|
B:HIS104
|
3.8
|
11.8
|
1.0
|
NE2
|
B:HIS104
|
4.1
|
10.3
|
1.0
|
NE2
|
B:HIS95
|
4.1
|
14.6
|
1.0
|
NE2
|
B:HIS113
|
4.1
|
12.5
|
1.0
|
CB
|
B:ASP116
|
4.2
|
9.3
|
1.0
|
CD2
|
B:HIS95
|
4.2
|
15.5
|
1.0
|
CD2
|
B:HIS113
|
4.2
|
11.8
|
1.0
|
CD2
|
B:HIS104
|
4.2
|
11.1
|
1.0
|
CD2
|
B:LEU164
|
4.6
|
18.6
|
1.0
|
N
|
B:GLY105
|
4.7
|
9.6
|
1.0
|
CA
|
B:ASP116
|
4.7
|
8.9
|
1.0
|
CA
|
B:HIS113
|
4.7
|
10.7
|
1.0
|
C
|
B:HIS104
|
4.8
|
12.2
|
1.0
|
N
|
B:HIS104
|
4.8
|
11.2
|
1.0
|
N
|
B:HIS113
|
4.8
|
11.2
|
1.0
|
CD2
|
B:HIS70
|
4.9
|
10.4
|
1.0
|
N
|
B:ASP116
|
4.9
|
9.1
|
1.0
|
O
|
B:LYS103
|
4.9
|
11.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1z9n
Go back to
Zinc Binding Sites List in 1z9n
Zinc binding site 3 out
of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:11.2
occ:1.00
|
OD1
|
C:ASP116
|
2.0
|
9.2
|
1.0
|
ND1
|
C:HIS95
|
2.1
|
12.9
|
1.0
|
ND1
|
C:HIS113
|
2.1
|
13.2
|
1.0
|
ND1
|
C:HIS104
|
2.1
|
9.4
|
1.0
|
CG
|
C:ASP116
|
2.7
|
9.5
|
1.0
|
OD2
|
C:ASP116
|
2.8
|
10.5
|
1.0
|
CE1
|
C:HIS104
|
2.9
|
10.2
|
1.0
|
CE1
|
C:HIS95
|
2.9
|
14.7
|
1.0
|
CE1
|
C:HIS113
|
2.9
|
13.8
|
1.0
|
CG
|
C:HIS113
|
3.1
|
14.2
|
1.0
|
CG
|
C:HIS95
|
3.1
|
13.2
|
1.0
|
CG
|
C:HIS104
|
3.2
|
10.0
|
1.0
|
CB
|
C:HIS113
|
3.5
|
11.6
|
1.0
|
CB
|
C:HIS95
|
3.6
|
14.6
|
1.0
|
CB
|
C:HIS104
|
3.6
|
11.3
|
1.0
|
CA
|
C:HIS104
|
3.8
|
12.4
|
1.0
|
NE2
|
C:HIS95
|
4.1
|
13.9
|
1.0
|
NE2
|
C:HIS104
|
4.1
|
9.9
|
1.0
|
NE2
|
C:HIS113
|
4.1
|
12.2
|
1.0
|
CB
|
C:ASP116
|
4.2
|
8.9
|
1.0
|
CD2
|
C:HIS95
|
4.2
|
14.1
|
1.0
|
CD2
|
C:HIS113
|
4.2
|
13.0
|
1.0
|
CD2
|
C:HIS104
|
4.2
|
9.4
|
1.0
|
CD2
|
C:LEU164
|
4.6
|
17.3
|
1.0
|
CA
|
C:ASP116
|
4.7
|
9.1
|
1.0
|
N
|
C:GLY105
|
4.7
|
11.0
|
1.0
|
CA
|
C:HIS113
|
4.7
|
12.2
|
1.0
|
N
|
C:HIS104
|
4.7
|
12.1
|
1.0
|
C
|
C:HIS104
|
4.8
|
12.5
|
1.0
|
N
|
C:HIS113
|
4.8
|
12.9
|
1.0
|
CD2
|
C:HIS70
|
4.8
|
10.3
|
1.0
|
N
|
C:ASP116
|
4.9
|
9.7
|
1.0
|
O
|
C:LYS103
|
4.9
|
14.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1z9n
Go back to
Zinc Binding Sites List in 1z9n
Zinc binding site 4 out
of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:13.7
occ:1.00
|
OD1
|
D:ASP116
|
2.0
|
11.6
|
1.0
|
ND1
|
D:HIS95
|
2.0
|
10.9
|
1.0
|
ND1
|
D:HIS113
|
2.1
|
13.2
|
1.0
|
ND1
|
D:HIS104
|
2.1
|
12.7
|
1.0
|
CG
|
D:ASP116
|
2.7
|
9.1
|
1.0
|
OD2
|
D:ASP116
|
2.8
|
12.9
|
1.0
|
CE1
|
D:HIS104
|
2.9
|
13.0
|
1.0
|
CE1
|
D:HIS95
|
2.9
|
13.3
|
1.0
|
CE1
|
D:HIS113
|
3.0
|
17.1
|
1.0
|
CG
|
D:HIS113
|
3.1
|
12.8
|
1.0
|
CG
|
D:HIS95
|
3.1
|
14.7
|
1.0
|
CG
|
D:HIS104
|
3.2
|
11.3
|
1.0
|
CB
|
D:HIS113
|
3.5
|
13.3
|
1.0
|
CB
|
D:HIS95
|
3.5
|
17.1
|
1.0
|
CB
|
D:HIS104
|
3.6
|
11.7
|
1.0
|
CA
|
D:HIS104
|
3.8
|
12.0
|
1.0
|
NE2
|
D:HIS95
|
4.1
|
17.9
|
1.0
|
NE2
|
D:HIS104
|
4.1
|
11.1
|
1.0
|
NE2
|
D:HIS113
|
4.1
|
15.6
|
1.0
|
CB
|
D:ASP116
|
4.2
|
12.4
|
1.0
|
CD2
|
D:HIS95
|
4.2
|
16.2
|
1.0
|
CD2
|
D:HIS113
|
4.2
|
15.7
|
1.0
|
CD2
|
D:HIS104
|
4.2
|
12.9
|
1.0
|
CD2
|
D:LEU164
|
4.5
|
15.0
|
1.0
|
CA
|
D:ASP116
|
4.7
|
11.8
|
1.0
|
N
|
D:GLY105
|
4.7
|
13.3
|
1.0
|
CA
|
D:HIS113
|
4.7
|
13.8
|
1.0
|
N
|
D:HIS104
|
4.8
|
12.9
|
1.0
|
CD2
|
D:HIS70
|
4.8
|
15.1
|
1.0
|
C
|
D:HIS104
|
4.8
|
13.5
|
1.0
|
N
|
D:HIS113
|
4.8
|
15.6
|
1.0
|
N
|
D:ASP116
|
4.9
|
13.4
|
1.0
|
CG
|
D:HIS70
|
5.0
|
15.2
|
1.0
|
|
Reference:
I.Toro,
C.Petrutz,
F.Pacello,
M.D'orazio,
A.Battistoni,
K.Djinovic-Carugo.
Structural Basis of Heme Binding in the Cu,Zn Superoxide Dismutase From Haemophilus Ducreyi. J.Mol.Biol. V. 386 406 2009.
ISSN: ISSN 0022-2836
PubMed: 19103206
DOI: 10.1016/J.JMB.2008.12.004
Page generated: Wed Oct 16 21:09:56 2024
|