Iron in PDB 1y07: Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Enzymatic activity of Crystal Structure of the Superoxide Reductase From Treponema Pallidum
All present enzymatic activity of Crystal Structure of the Superoxide Reductase From Treponema Pallidum:
1.15.1.2;
Protein crystallography data
The structure of Crystal Structure of the Superoxide Reductase From Treponema Pallidum, PDB code: 1y07
was solved by
T.Santos-Silva,
J.Trincao,
A.L.Carvalho,
C.Bonifacio,
F.Auchere,
J.Moura,
M.J.Romao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.25 /
1.55
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.311,
59.946,
65.520,
90.00,
104.96,
90.00
|
R / Rfree (%)
|
18.2 /
23.5
|
Other elements in 1y07:
The structure of Crystal Structure of the Superoxide Reductase From Treponema Pallidum also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
(pdb code 1y07). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of the Superoxide Reductase From Treponema Pallidum, PDB code: 1y07:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 1y07
Go back to
Iron Binding Sites List in 1y07
Iron binding site 1 out
of 5 in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Superoxide Reductase From Treponema Pallidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe130
b:22.7
occ:1.00
|
NE2
|
A:HIS70
|
2.2
|
13.8
|
1.0
|
NE2
|
A:HIS50
|
2.2
|
10.5
|
1.0
|
ND1
|
A:HIS122
|
2.3
|
13.0
|
1.0
|
SG
|
A:CYS119
|
2.3
|
9.5
|
1.0
|
NE2
|
A:HIS76
|
2.4
|
11.4
|
1.0
|
CE1
|
A:HIS70
|
2.9
|
13.9
|
1.0
|
CE1
|
A:HIS50
|
3.0
|
10.6
|
1.0
|
CE1
|
A:HIS76
|
3.2
|
16.6
|
1.0
|
CE1
|
A:HIS122
|
3.2
|
14.2
|
1.0
|
CG
|
A:HIS122
|
3.3
|
12.5
|
1.0
|
CD2
|
A:HIS70
|
3.4
|
13.9
|
1.0
|
CD2
|
A:HIS76
|
3.4
|
14.1
|
1.0
|
CD2
|
A:HIS50
|
3.4
|
13.8
|
1.0
|
CB
|
A:CYS119
|
3.4
|
9.4
|
1.0
|
CB
|
A:HIS122
|
3.5
|
11.2
|
1.0
|
ND1
|
A:HIS70
|
4.1
|
13.7
|
1.0
|
ND1
|
A:HIS50
|
4.1
|
14.7
|
1.0
|
ND1
|
A:HIS76
|
4.3
|
14.8
|
1.0
|
O
|
A:HOH620
|
4.3
|
40.3
|
1.0
|
CG
|
A:HIS70
|
4.3
|
11.1
|
1.0
|
NE2
|
A:HIS122
|
4.4
|
14.7
|
1.0
|
CG
|
A:HIS50
|
4.4
|
10.3
|
1.0
|
CD2
|
A:HIS122
|
4.4
|
15.7
|
1.0
|
CG
|
A:HIS76
|
4.4
|
11.0
|
1.0
|
N
|
A:HIS122
|
4.5
|
11.6
|
1.0
|
CA
|
A:HIS122
|
4.7
|
10.2
|
1.0
|
CA
|
A:CYS119
|
4.8
|
8.7
|
1.0
|
CB
|
A:LEU121
|
4.9
|
11.5
|
1.0
|
|
Iron binding site 2 out
of 5 in 1y07
Go back to
Iron Binding Sites List in 1y07
Iron binding site 2 out
of 5 in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Superoxide Reductase From Treponema Pallidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:22.4
occ:0.80
|
O
|
A:HOH565
|
3.3
|
30.3
|
1.0
|
NE2
|
A:GLN111
|
3.3
|
5.8
|
1.0
|
O
|
A:HOH509
|
3.3
|
16.2
|
1.0
|
NE2
|
C:GLN111
|
3.4
|
7.0
|
1.0
|
O
|
A:HOH589
|
3.4
|
30.4
|
1.0
|
O
|
C:HOH503
|
3.4
|
17.2
|
1.0
|
CG
|
C:GLN111
|
3.9
|
7.4
|
1.0
|
CG2
|
C:VAL56
|
3.9
|
8.4
|
1.0
|
CG
|
A:GLN111
|
4.0
|
5.1
|
1.0
|
CG2
|
A:VAL56
|
4.0
|
7.9
|
1.0
|
CD
|
C:GLN111
|
4.1
|
6.6
|
1.0
|
CD
|
A:GLN111
|
4.2
|
6.4
|
1.0
|
CB
|
A:VAL56
|
4.4
|
8.3
|
1.0
|
CG1
|
A:VAL56
|
4.4
|
7.9
|
1.0
|
CG1
|
C:VAL56
|
4.4
|
8.0
|
1.0
|
CG1
|
A:VAL112
|
4.4
|
8.0
|
1.0
|
CG1
|
C:VAL112
|
4.5
|
5.9
|
1.0
|
CB
|
C:VAL56
|
4.5
|
7.5
|
1.0
|
|
Iron binding site 3 out
of 5 in 1y07
Go back to
Iron Binding Sites List in 1y07
Iron binding site 3 out
of 5 in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Superoxide Reductase From Treponema Pallidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe130
b:37.5
occ:1.00
|
NE2
|
B:HIS76
|
2.1
|
19.3
|
1.0
|
ND1
|
B:HIS122
|
2.1
|
21.4
|
1.0
|
SG
|
B:CYS119
|
2.1
|
22.1
|
1.0
|
NE2
|
B:HIS50
|
2.3
|
18.5
|
1.0
|
NE2
|
B:HIS70
|
2.4
|
20.8
|
1.0
|
CE1
|
B:HIS122
|
3.0
|
19.9
|
1.0
|
CE1
|
B:HIS50
|
3.0
|
19.3
|
1.0
|
CD2
|
B:HIS76
|
3.1
|
19.9
|
1.0
|
CE1
|
B:HIS76
|
3.1
|
19.4
|
1.0
|
CE1
|
B:HIS70
|
3.2
|
21.3
|
1.0
|
CG
|
B:HIS122
|
3.2
|
20.0
|
1.0
|
CB
|
B:CYS119
|
3.4
|
19.4
|
1.0
|
CD2
|
B:HIS50
|
3.4
|
17.0
|
1.0
|
CD2
|
B:HIS70
|
3.5
|
18.3
|
1.0
|
CB
|
B:HIS122
|
3.6
|
19.3
|
1.0
|
NE2
|
B:HIS122
|
4.1
|
19.4
|
1.0
|
N
|
B:HIS122
|
4.1
|
19.8
|
1.0
|
ND1
|
B:HIS76
|
4.2
|
19.0
|
1.0
|
CG
|
B:HIS76
|
4.2
|
20.1
|
1.0
|
CD2
|
B:HIS122
|
4.2
|
19.1
|
1.0
|
ND1
|
B:HIS50
|
4.3
|
17.9
|
1.0
|
O
|
B:HOH192
|
4.3
|
34.9
|
1.0
|
ND1
|
B:HIS70
|
4.4
|
21.1
|
1.0
|
CG
|
B:HIS50
|
4.5
|
18.0
|
1.0
|
CA
|
B:HIS122
|
4.5
|
19.5
|
1.0
|
CG
|
B:HIS70
|
4.6
|
20.2
|
1.0
|
CB
|
B:LEU121
|
4.6
|
20.8
|
1.0
|
CA
|
B:CYS119
|
4.7
|
19.1
|
1.0
|
C
|
B:LEU121
|
4.9
|
20.1
|
1.0
|
N
|
B:LEU121
|
4.9
|
20.1
|
1.0
|
|
Iron binding site 4 out
of 5 in 1y07
Go back to
Iron Binding Sites List in 1y07
Iron binding site 4 out
of 5 in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Superoxide Reductase From Treponema Pallidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe130
b:23.6
occ:1.00
|
NE2
|
C:HIS50
|
2.1
|
12.2
|
1.0
|
ND1
|
C:HIS122
|
2.2
|
9.7
|
1.0
|
NE2
|
C:HIS70
|
2.2
|
11.4
|
1.0
|
NE2
|
C:HIS76
|
2.3
|
12.1
|
1.0
|
SG
|
C:CYS119
|
2.3
|
10.9
|
1.0
|
CE1
|
C:HIS50
|
3.0
|
15.6
|
1.0
|
CE1
|
C:HIS122
|
3.1
|
13.1
|
1.0
|
CD2
|
C:HIS50
|
3.1
|
13.5
|
1.0
|
CD2
|
C:HIS70
|
3.1
|
11.0
|
1.0
|
CE1
|
C:HIS76
|
3.2
|
14.2
|
1.0
|
CG
|
C:HIS122
|
3.2
|
13.4
|
1.0
|
CD2
|
C:HIS76
|
3.2
|
11.9
|
1.0
|
CE1
|
C:HIS70
|
3.3
|
12.8
|
1.0
|
CB
|
C:CYS119
|
3.5
|
9.6
|
1.0
|
CB
|
C:HIS122
|
3.6
|
14.4
|
1.0
|
ND1
|
C:HIS50
|
4.1
|
16.1
|
1.0
|
CG
|
C:HIS50
|
4.2
|
12.1
|
1.0
|
NE2
|
C:HIS122
|
4.3
|
14.5
|
1.0
|
N
|
C:HIS122
|
4.3
|
14.0
|
1.0
|
CD2
|
C:HIS122
|
4.3
|
14.2
|
1.0
|
CG
|
C:HIS70
|
4.3
|
10.7
|
1.0
|
ND1
|
C:HIS76
|
4.3
|
11.1
|
1.0
|
ND1
|
C:HIS70
|
4.3
|
10.2
|
1.0
|
O
|
C:HOH609
|
4.4
|
33.5
|
1.0
|
CG
|
C:HIS76
|
4.4
|
12.8
|
1.0
|
CA
|
C:HIS122
|
4.6
|
13.4
|
1.0
|
CB
|
C:LEU121
|
4.6
|
15.1
|
1.0
|
CA
|
C:CYS119
|
4.8
|
10.2
|
1.0
|
CD1
|
C:ILE78
|
5.0
|
11.6
|
1.0
|
|
Iron binding site 5 out
of 5 in 1y07
Go back to
Iron Binding Sites List in 1y07
Iron binding site 5 out
of 5 in the Crystal Structure of the Superoxide Reductase From Treponema Pallidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Superoxide Reductase From Treponema Pallidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe130
b:38.5
occ:1.00
|
NE2
|
D:HIS50
|
2.2
|
15.8
|
1.0
|
ND1
|
D:HIS122
|
2.2
|
19.1
|
1.0
|
NE2
|
D:HIS76
|
2.2
|
29.4
|
1.0
|
NE2
|
D:HIS70
|
2.4
|
16.5
|
1.0
|
SG
|
D:CYS119
|
2.4
|
21.0
|
1.0
|
O
|
D:HOH192
|
2.7
|
35.0
|
1.0
|
CE1
|
D:HIS50
|
3.0
|
18.9
|
1.0
|
CE1
|
D:HIS122
|
3.1
|
19.7
|
1.0
|
CE1
|
D:HIS76
|
3.1
|
30.6
|
1.0
|
CG
|
D:HIS122
|
3.2
|
17.6
|
1.0
|
CE1
|
D:HIS70
|
3.3
|
19.1
|
1.0
|
CD2
|
D:HIS76
|
3.3
|
29.6
|
1.0
|
CD2
|
D:HIS50
|
3.3
|
17.2
|
1.0
|
CD2
|
D:HIS70
|
3.5
|
20.2
|
1.0
|
CB
|
D:HIS122
|
3.6
|
16.2
|
1.0
|
CB
|
D:CYS119
|
3.6
|
18.3
|
1.0
|
ND1
|
D:HIS50
|
4.1
|
18.9
|
1.0
|
NE2
|
D:HIS122
|
4.3
|
17.9
|
1.0
|
ND1
|
D:HIS76
|
4.3
|
30.6
|
1.0
|
CG
|
D:HIS50
|
4.3
|
16.8
|
1.0
|
CD2
|
D:HIS122
|
4.3
|
17.3
|
1.0
|
CG
|
D:HIS76
|
4.4
|
29.1
|
1.0
|
ND1
|
D:HIS70
|
4.4
|
19.6
|
1.0
|
N
|
D:HIS122
|
4.6
|
18.0
|
1.0
|
CG
|
D:HIS70
|
4.6
|
21.3
|
1.0
|
CA
|
D:HIS122
|
4.7
|
17.0
|
1.0
|
CB
|
D:LEU121
|
4.9
|
20.8
|
1.0
|
CA
|
D:CYS119
|
5.0
|
17.7
|
1.0
|
|
Reference:
T.Santos-Silva,
J.Trincao,
A.L.Carvalho,
C.Bonifacio,
F.Auchere,
P.Raleiras,
I.Moura,
J.Moura,
M.J.Romao.
The First Crystal Structure of Class III Superoxide Reductase From Treponema Pallidum. J.Biol.Inorg.Chem. V. 11 548 2006.
ISSN: ISSN 0949-8257
PubMed: 16791639
DOI: 10.1007/S00775-006-0104-Y
Page generated: Sat Aug 3 17:08:47 2024
|