Iron in PDB 6qka: Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Enzymatic activity of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
All present enzymatic activity of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase:
1.13.11.55;
Protein crystallography data
The structure of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase, PDB code: 6qka
was solved by
C.Frazao,
A.Klezin,
U.Poell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
76.95 /
2.10
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
161.913,
161.913,
153.901,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.3 /
20.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
(pdb code 6qka). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase, PDB code: 6qka:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 1 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:0.9
occ:1.00
|
OE2
|
A:GLU114
|
2.3
|
42.4
|
1.0
|
O
|
A:HOH622
|
2.5
|
51.6
|
1.0
|
NE2
|
A:HIS90
|
2.7
|
63.3
|
1.0
|
O
|
A:HOH618
|
2.9
|
76.4
|
1.0
|
CD
|
A:GLU114
|
3.0
|
37.2
|
1.0
|
OE1
|
A:GLU114
|
3.1
|
42.7
|
1.0
|
NE2
|
A:HIS86
|
3.1
|
39.1
|
1.0
|
CE1
|
A:HIS90
|
3.3
|
62.2
|
1.0
|
O
|
A:HOH527
|
3.9
|
31.1
|
1.0
|
CD2
|
A:HIS90
|
4.0
|
62.3
|
1.0
|
CD2
|
A:HIS86
|
4.0
|
36.9
|
1.0
|
CE1
|
A:HIS86
|
4.1
|
38.5
|
1.0
|
OD1
|
A:ASN9
|
4.4
|
49.2
|
1.0
|
CG
|
A:GLU114
|
4.4
|
30.1
|
1.0
|
ND1
|
A:HIS90
|
4.5
|
63.5
|
1.0
|
OG1
|
A:THR78
|
4.7
|
26.0
|
1.0
|
CB
|
A:ASN9
|
4.7
|
25.1
|
1.0
|
CG
|
A:ASN9
|
4.9
|
39.3
|
1.0
|
CG
|
A:HIS90
|
4.9
|
58.7
|
1.0
|
CA
|
A:GLY208
|
5.0
|
23.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 2 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:0.5
occ:1.00
|
OE2
|
B:GLU114
|
2.3
|
40.5
|
1.0
|
NE2
|
B:HIS90
|
2.6
|
46.5
|
1.0
|
NE2
|
B:HIS86
|
2.8
|
38.2
|
1.0
|
CD
|
B:GLU114
|
3.0
|
39.5
|
1.0
|
OE1
|
B:GLU114
|
3.0
|
44.2
|
1.0
|
O
|
B:HOH616
|
3.1
|
78.0
|
1.0
|
O
|
B:HOH621
|
3.2
|
64.2
|
1.0
|
CE1
|
B:HIS90
|
3.4
|
47.1
|
1.0
|
CD2
|
B:HIS86
|
3.5
|
34.8
|
1.0
|
CD2
|
B:HIS90
|
3.6
|
46.0
|
1.0
|
O
|
B:HOH552
|
3.7
|
28.8
|
1.0
|
CE1
|
B:HIS86
|
3.8
|
37.6
|
1.0
|
CG
|
B:GLU114
|
4.5
|
34.1
|
1.0
|
OG1
|
B:THR78
|
4.6
|
25.9
|
1.0
|
ND1
|
B:HIS90
|
4.6
|
45.8
|
1.0
|
CG
|
B:HIS86
|
4.7
|
36.1
|
1.0
|
CG
|
B:HIS90
|
4.7
|
45.4
|
1.0
|
ND1
|
B:HIS86
|
4.8
|
34.4
|
1.0
|
CE
|
B:MET89
|
4.9
|
45.1
|
1.0
|
CB
|
B:ALA7
|
5.0
|
27.8
|
1.0
|
|
Iron binding site 3 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 3 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:0.2
occ:1.00
|
OE2
|
C:GLU114
|
2.3
|
47.1
|
1.0
|
NE2
|
C:HIS90
|
2.4
|
58.2
|
1.0
|
O
|
C:HOH609
|
2.5
|
59.9
|
1.0
|
NE2
|
C:HIS86
|
2.6
|
37.7
|
1.0
|
O
|
C:HOH590
|
2.6
|
73.5
|
1.0
|
OE1
|
C:GLU114
|
2.9
|
39.3
|
1.0
|
CD
|
C:GLU114
|
2.9
|
40.8
|
1.0
|
CE1
|
C:HIS90
|
3.2
|
56.9
|
1.0
|
CD2
|
C:HIS86
|
3.4
|
37.6
|
1.0
|
CD2
|
C:HIS90
|
3.5
|
56.7
|
1.0
|
CE1
|
C:HIS86
|
3.6
|
37.5
|
1.0
|
O
|
C:HOH551
|
4.0
|
33.2
|
1.0
|
ND1
|
C:HIS90
|
4.4
|
55.8
|
1.0
|
CG
|
C:GLU114
|
4.4
|
28.6
|
1.0
|
CG
|
C:HIS90
|
4.5
|
51.2
|
1.0
|
CG
|
C:HIS86
|
4.6
|
40.0
|
1.0
|
ND1
|
C:HIS86
|
4.7
|
38.3
|
1.0
|
OG1
|
C:THR78
|
4.7
|
29.5
|
1.0
|
OD1
|
C:ASN9
|
4.7
|
48.7
|
1.0
|
CA
|
C:GLY208
|
4.8
|
23.8
|
1.0
|
CE
|
C:MET89
|
4.9
|
52.9
|
1.0
|
CB
|
C:ALA7
|
5.0
|
21.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 4 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:0.3
occ:1.00
|
O
|
D:HOH612
|
2.3
|
66.5
|
1.0
|
OE2
|
D:GLU114
|
2.4
|
37.4
|
1.0
|
NE2
|
D:HIS90
|
2.6
|
60.4
|
1.0
|
O
|
D:HOH615
|
2.7
|
68.0
|
1.0
|
NE2
|
D:HIS86
|
2.8
|
41.6
|
1.0
|
OE1
|
D:GLU114
|
3.0
|
41.3
|
1.0
|
CD
|
D:GLU114
|
3.1
|
39.7
|
1.0
|
CE1
|
D:HIS90
|
3.4
|
62.1
|
1.0
|
CD2
|
D:HIS86
|
3.6
|
36.6
|
1.0
|
CD2
|
D:HIS90
|
3.6
|
59.4
|
1.0
|
CE1
|
D:HIS86
|
3.8
|
36.0
|
1.0
|
O
|
D:HOH567
|
3.9
|
29.0
|
1.0
|
CG
|
D:GLU114
|
4.6
|
35.6
|
1.0
|
ND1
|
D:HIS90
|
4.6
|
60.7
|
1.0
|
OG1
|
D:THR78
|
4.7
|
26.1
|
1.0
|
CG
|
D:HIS90
|
4.7
|
54.8
|
1.0
|
CG
|
D:HIS86
|
4.8
|
38.0
|
1.0
|
ND1
|
D:HIS86
|
4.9
|
37.8
|
1.0
|
CE
|
D:MET89
|
4.9
|
47.7
|
1.0
|
OD1
|
D:ASN9
|
4.9
|
49.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 5 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:0.3
occ:1.00
|
O
|
E:HOH606
|
2.3
|
65.7
|
1.0
|
OE2
|
E:GLU114
|
2.5
|
48.2
|
1.0
|
O
|
E:HOH615
|
2.6
|
62.0
|
1.0
|
NE2
|
E:HIS90
|
2.6
|
53.6
|
1.0
|
NE2
|
E:HIS86
|
3.0
|
30.9
|
1.0
|
OE1
|
E:GLU114
|
3.1
|
46.4
|
1.0
|
CD
|
E:GLU114
|
3.1
|
43.3
|
1.0
|
CE1
|
E:HIS90
|
3.3
|
50.1
|
1.0
|
CD2
|
E:HIS90
|
3.8
|
50.5
|
1.0
|
CD2
|
E:HIS86
|
3.8
|
30.9
|
1.0
|
O
|
E:HOH566
|
3.9
|
26.6
|
1.0
|
CE1
|
E:HIS86
|
4.0
|
26.6
|
1.0
|
ND1
|
E:HIS90
|
4.6
|
50.7
|
1.0
|
CG
|
E:GLU114
|
4.6
|
31.2
|
1.0
|
OD1
|
E:ASN9
|
4.7
|
50.8
|
1.0
|
OG1
|
E:THR78
|
4.8
|
23.6
|
1.0
|
CE
|
E:MET89
|
4.8
|
46.5
|
1.0
|
CG
|
E:HIS90
|
4.8
|
46.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 6qka
Go back to
Iron Binding Sites List in 6qka
Iron binding site 6 out
of 6 in the Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:1.0
occ:1.00
|
OE2
|
F:GLU114
|
2.3
|
46.0
|
1.0
|
O
|
F:HOH598
|
2.4
|
45.5
|
1.0
|
CE1
|
F:HIS90
|
2.5
|
56.7
|
1.0
|
NE2
|
F:HIS86
|
2.6
|
38.4
|
1.0
|
O
|
F:HOH621
|
2.8
|
73.7
|
1.0
|
OE1
|
F:GLU114
|
3.0
|
40.4
|
1.0
|
CD
|
F:GLU114
|
3.0
|
38.1
|
1.0
|
NE2
|
F:HIS90
|
3.1
|
53.4
|
1.0
|
CD2
|
F:HIS86
|
3.4
|
35.4
|
1.0
|
CE1
|
F:HIS86
|
3.6
|
38.9
|
1.0
|
ND1
|
F:HIS90
|
3.7
|
51.6
|
1.0
|
O
|
F:HOH525
|
3.7
|
26.7
|
1.0
|
CD2
|
F:HIS90
|
4.4
|
51.4
|
1.0
|
CG
|
F:GLU114
|
4.5
|
34.8
|
1.0
|
OG1
|
F:THR78
|
4.6
|
25.4
|
1.0
|
CG
|
F:HIS86
|
4.6
|
38.0
|
1.0
|
ND1
|
F:HIS86
|
4.6
|
37.6
|
1.0
|
CG
|
F:HIS90
|
4.7
|
50.3
|
1.0
|
CE
|
F:MET89
|
4.9
|
46.5
|
1.0
|
OD1
|
F:ASN9
|
4.9
|
53.9
|
1.0
|
CA
|
F:GLY208
|
5.0
|
27.0
|
1.0
|
CB
|
F:ALA7
|
5.0
|
21.7
|
1.0
|
|
Reference:
C.Frazao,
A.Klezin.
Multiple Sulfane Modifications in Active-Site Cysteine Thiols of Two Sulfur Oxygenase Reductases and Analysis of Substrate/Product Channels To Be Published.
Page generated: Wed Aug 7 07:54:46 2024
|