Iron in PDB 6qpa: Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
Enzymatic activity of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
All present enzymatic activity of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase:
1.13.11.55;
Protein crystallography data
The structure of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase, PDB code: 6qpa
was solved by
C.Frazao,
A.Klezin,
U.Poell,
A.Veith,
P.Ruehl,
R.Coelho,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
83.70 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
200.840,
212.450,
215.980,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
20
|
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Iron atom in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
(pdb code 6qpa). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase, PDB code: 6qpa:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 1 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:40.5
occ:0.40
|
O
|
A:HOH564
|
2.1
|
52.3
|
1.0
|
OE2
|
A:GLU116
|
2.1
|
50.2
|
1.0
|
NE2
|
A:HIS88
|
2.2
|
41.1
|
1.0
|
O
|
A:HOH659
|
2.3
|
50.9
|
1.0
|
NE2
|
A:HIS92
|
2.5
|
57.7
|
1.0
|
CD
|
A:GLU116
|
2.8
|
36.1
|
1.0
|
OE1
|
A:GLU116
|
2.8
|
41.3
|
1.0
|
CE1
|
A:HIS88
|
2.9
|
40.5
|
1.0
|
CD2
|
A:HIS92
|
3.4
|
52.2
|
1.0
|
CD2
|
A:HIS88
|
3.4
|
38.9
|
1.0
|
CE1
|
A:HIS92
|
3.5
|
57.7
|
1.0
|
O
|
A:HOH518
|
3.8
|
39.8
|
1.0
|
O
|
A:HOH675
|
4.0
|
58.1
|
1.0
|
ND1
|
A:HIS88
|
4.2
|
40.8
|
1.0
|
CG
|
A:GLU116
|
4.2
|
33.1
|
1.0
|
OG1
|
A:THR80
|
4.3
|
28.3
|
1.0
|
CG
|
A:HIS88
|
4.4
|
36.1
|
1.0
|
CG
|
A:HIS92
|
4.5
|
47.6
|
1.0
|
ND1
|
A:HIS92
|
4.6
|
52.0
|
1.0
|
CA
|
A:GLY208
|
4.7
|
31.6
|
1.0
|
ND2
|
A:ASN11
|
4.7
|
51.6
|
1.0
|
CE
|
A:MET91
|
4.9
|
44.1
|
1.0
|
CB
|
A:ALA9
|
5.0
|
25.7
|
1.0
|
|
Iron binding site 2 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 2 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:37.4
occ:0.40
|
O
|
B:HOH609
|
2.1
|
46.1
|
1.0
|
NE2
|
B:HIS88
|
2.2
|
38.5
|
1.0
|
NE2
|
B:HIS92
|
2.2
|
54.0
|
1.0
|
OE2
|
B:GLU116
|
2.3
|
49.5
|
1.0
|
O
|
B:HOH633
|
2.3
|
50.5
|
1.0
|
OE1
|
B:GLU116
|
2.6
|
41.1
|
1.0
|
CD
|
B:GLU116
|
2.7
|
40.1
|
1.0
|
CE1
|
B:HIS88
|
2.8
|
32.2
|
1.0
|
CE1
|
B:HIS92
|
3.1
|
54.0
|
1.0
|
CD2
|
B:HIS92
|
3.3
|
56.0
|
1.0
|
CD2
|
B:HIS88
|
3.4
|
32.9
|
1.0
|
O
|
B:HOH515
|
3.9
|
32.8
|
1.0
|
ND1
|
B:HIS88
|
4.1
|
37.6
|
1.0
|
CG
|
B:GLU116
|
4.2
|
34.9
|
1.0
|
ND1
|
B:HIS92
|
4.2
|
50.4
|
1.0
|
CG
|
B:HIS88
|
4.3
|
36.9
|
1.0
|
CG
|
B:HIS92
|
4.4
|
47.5
|
1.0
|
OG1
|
B:THR80
|
4.4
|
31.1
|
1.0
|
CA
|
B:GLY208
|
4.5
|
32.8
|
1.0
|
CE
|
B:MET91
|
4.8
|
41.1
|
1.0
|
ND2
|
B:ASN11
|
4.8
|
55.8
|
1.0
|
CB
|
B:ALA9
|
5.0
|
26.4
|
1.0
|
|
Iron binding site 3 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 3 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:44.1
occ:0.40
|
NE2
|
C:HIS92
|
2.1
|
62.3
|
1.0
|
NE2
|
C:HIS88
|
2.2
|
45.8
|
1.0
|
OE2
|
C:GLU116
|
2.4
|
53.9
|
1.0
|
O
|
C:HOH608
|
2.4
|
68.1
|
1.0
|
OE1
|
C:GLU116
|
2.6
|
36.4
|
1.0
|
CD
|
C:GLU116
|
2.8
|
46.2
|
1.0
|
CE1
|
C:HIS88
|
2.8
|
43.3
|
1.0
|
CE1
|
C:HIS92
|
3.0
|
58.1
|
1.0
|
CD2
|
C:HIS92
|
3.2
|
58.8
|
1.0
|
CD2
|
C:HIS88
|
3.4
|
44.2
|
1.0
|
O
|
C:HOH503
|
3.9
|
42.2
|
1.0
|
ND1
|
C:HIS88
|
4.1
|
46.9
|
1.0
|
ND1
|
C:HIS92
|
4.2
|
55.4
|
1.0
|
CG
|
C:HIS92
|
4.3
|
56.0
|
1.0
|
CG
|
C:GLU116
|
4.3
|
40.6
|
1.0
|
CG
|
C:HIS88
|
4.4
|
44.0
|
1.0
|
CA
|
C:GLY208
|
4.5
|
34.7
|
1.0
|
OG1
|
C:THR80
|
4.6
|
35.0
|
1.0
|
ND2
|
C:ASN11
|
4.8
|
57.0
|
1.0
|
CE
|
C:MET91
|
4.8
|
53.3
|
1.0
|
|
Iron binding site 4 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 4 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:61.1
occ:0.40
|
NE2
|
D:HIS92
|
2.2
|
70.1
|
1.0
|
OE2
|
D:GLU116
|
2.4
|
59.1
|
1.0
|
NE2
|
D:HIS88
|
2.5
|
61.7
|
1.0
|
OE1
|
D:GLU116
|
2.8
|
58.1
|
1.0
|
O
|
D:HOH598
|
2.8
|
61.0
|
1.0
|
CD
|
D:GLU116
|
2.9
|
55.7
|
1.0
|
CE1
|
D:HIS92
|
3.2
|
68.0
|
1.0
|
CD2
|
D:HIS92
|
3.2
|
72.9
|
1.0
|
CE1
|
D:HIS88
|
3.3
|
58.2
|
1.0
|
CD2
|
D:HIS88
|
3.7
|
57.5
|
1.0
|
O
|
D:HOH518
|
4.1
|
44.3
|
1.0
|
ND1
|
D:HIS92
|
4.3
|
70.7
|
1.0
|
CG
|
D:HIS92
|
4.4
|
70.0
|
1.0
|
CG
|
D:GLU116
|
4.4
|
47.9
|
1.0
|
ND1
|
D:HIS88
|
4.5
|
60.2
|
1.0
|
OG1
|
D:THR80
|
4.5
|
43.4
|
1.0
|
CA
|
D:GLY208
|
4.6
|
48.3
|
1.0
|
CG
|
D:HIS88
|
4.7
|
57.8
|
1.0
|
CE
|
D:MET91
|
4.8
|
69.7
|
1.0
|
ND2
|
D:ASN11
|
4.8
|
70.4
|
1.0
|
|
Iron binding site 5 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 5 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:50.0
occ:0.40
|
NE2
|
E:HIS92
|
2.1
|
65.6
|
1.0
|
O
|
E:HOH623
|
2.3
|
57.1
|
1.0
|
OE2
|
E:GLU116
|
2.3
|
45.6
|
1.0
|
NE2
|
E:HIS88
|
2.6
|
50.5
|
1.0
|
OE1
|
E:GLU116
|
2.8
|
45.4
|
1.0
|
CE1
|
E:HIS92
|
2.9
|
66.2
|
1.0
|
CD
|
E:GLU116
|
2.9
|
43.5
|
1.0
|
CD2
|
E:HIS92
|
3.2
|
65.2
|
1.0
|
CE1
|
E:HIS88
|
3.2
|
49.6
|
1.0
|
CD2
|
E:HIS88
|
3.7
|
46.7
|
1.0
|
O
|
E:HOH525
|
4.1
|
37.8
|
1.0
|
ND1
|
E:HIS92
|
4.1
|
64.5
|
1.0
|
CG
|
E:HIS92
|
4.3
|
60.2
|
1.0
|
CG
|
E:GLU116
|
4.4
|
35.4
|
1.0
|
ND1
|
E:HIS88
|
4.4
|
52.9
|
1.0
|
CA
|
E:GLY208
|
4.5
|
39.8
|
1.0
|
ND2
|
E:ASN11
|
4.5
|
65.8
|
1.0
|
O
|
E:HOH618
|
4.6
|
61.7
|
1.0
|
OG1
|
E:THR80
|
4.7
|
40.5
|
1.0
|
CG
|
E:HIS88
|
4.7
|
48.6
|
1.0
|
CE
|
E:MET91
|
4.8
|
55.6
|
1.0
|
|
Iron binding site 6 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 6 out
of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:50.1
occ:0.40
|
OE2
|
F:GLU116
|
2.2
|
61.3
|
1.0
|
NE2
|
F:HIS92
|
2.4
|
66.6
|
1.0
|
NE2
|
F:HIS88
|
2.4
|
50.8
|
1.0
|
O
|
F:HOH600
|
2.4
|
65.5
|
1.0
|
O
|
F:HOH598
|
2.6
|
76.2
|
1.0
|
OE1
|
F:GLU116
|
2.6
|
44.9
|
1.0
|
CD
|
F:GLU116
|
2.7
|
52.2
|
1.0
|
CE1
|
F:HIS88
|
3.0
|
50.3
|
1.0
|
CE1
|
F:HIS92
|
3.3
|
63.0
|
1.0
|
CD2
|
F:HIS92
|
3.4
|
64.6
|
1.0
|
CD2
|
F:HIS88
|
3.6
|
51.0
|
1.0
|
O
|
F:HOH511
|
3.8
|
43.1
|
1.0
|
CG
|
F:GLU116
|
4.2
|
46.6
|
1.0
|
ND1
|
F:HIS88
|
4.3
|
53.4
|
1.0
|
ND1
|
F:HIS92
|
4.4
|
63.7
|
1.0
|
CG
|
F:HIS92
|
4.5
|
62.3
|
1.0
|
CA
|
F:GLY208
|
4.5
|
43.8
|
1.0
|
ND2
|
F:ASN11
|
4.5
|
58.8
|
1.0
|
CG
|
F:HIS88
|
4.6
|
53.1
|
1.0
|
OG1
|
F:THR80
|
4.6
|
48.0
|
1.0
|
CE
|
F:MET91
|
5.0
|
74.1
|
1.0
|
|
Iron binding site 7 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 7 out
of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe401
b:38.5
occ:0.40
|
OE2
|
G:GLU116
|
2.2
|
42.8
|
1.0
|
NE2
|
G:HIS92
|
2.2
|
54.8
|
1.0
|
NE2
|
G:HIS88
|
2.3
|
38.2
|
1.0
|
O
|
G:HOH663
|
2.3
|
52.7
|
1.0
|
O
|
G:HOH683
|
2.4
|
48.9
|
1.0
|
OE1
|
G:GLU116
|
2.7
|
38.8
|
1.0
|
CD
|
G:GLU116
|
2.8
|
35.9
|
1.0
|
CE1
|
G:HIS88
|
2.9
|
36.5
|
1.0
|
CE1
|
G:HIS92
|
3.1
|
56.7
|
1.0
|
CD2
|
G:HIS92
|
3.3
|
51.7
|
1.0
|
CD2
|
G:HIS88
|
3.5
|
35.1
|
1.0
|
O
|
G:HOH551
|
4.0
|
26.5
|
1.0
|
ND1
|
G:HIS88
|
4.2
|
42.0
|
1.0
|
ND1
|
G:HIS92
|
4.3
|
49.8
|
1.0
|
CG
|
G:GLU116
|
4.3
|
27.1
|
1.0
|
O
|
G:HOH668
|
4.3
|
55.6
|
1.0
|
CG
|
G:HIS92
|
4.4
|
46.5
|
1.0
|
OG1
|
G:THR80
|
4.4
|
28.8
|
1.0
|
CG
|
G:HIS88
|
4.5
|
34.6
|
1.0
|
CA
|
G:GLY208
|
4.5
|
24.7
|
1.0
|
CE
|
G:MET91
|
4.7
|
42.0
|
1.0
|
ND2
|
G:ASN11
|
4.8
|
45.3
|
1.0
|
|
Iron binding site 8 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 8 out
of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe401
b:40.5
occ:0.40
|
NE2
|
H:HIS88
|
2.2
|
42.8
|
1.0
|
O
|
H:HOH637
|
2.2
|
55.7
|
1.0
|
NE2
|
H:HIS92
|
2.3
|
57.9
|
1.0
|
OE2
|
H:GLU116
|
2.3
|
46.0
|
1.0
|
OE1
|
H:GLU116
|
2.7
|
42.0
|
1.0
|
CD
|
H:GLU116
|
2.8
|
38.1
|
1.0
|
CE1
|
H:HIS88
|
2.9
|
39.4
|
1.0
|
CD2
|
H:HIS92
|
3.2
|
56.9
|
1.0
|
CE1
|
H:HIS92
|
3.3
|
57.5
|
1.0
|
CD2
|
H:HIS88
|
3.4
|
40.1
|
1.0
|
O
|
H:HOH502
|
3.8
|
32.0
|
1.0
|
O
|
H:HOH670
|
4.0
|
46.0
|
1.0
|
ND1
|
H:HIS88
|
4.1
|
40.5
|
1.0
|
OG1
|
H:THR80
|
4.3
|
30.0
|
1.0
|
CG
|
H:GLU116
|
4.3
|
29.8
|
1.0
|
ND1
|
H:HIS92
|
4.4
|
53.2
|
1.0
|
CG
|
H:HIS88
|
4.4
|
38.6
|
1.0
|
CG
|
H:HIS92
|
4.4
|
50.3
|
1.0
|
CA
|
H:GLY208
|
4.7
|
33.9
|
1.0
|
CE
|
H:MET91
|
4.8
|
40.4
|
1.0
|
ND2
|
H:ASN11
|
4.9
|
53.4
|
1.0
|
CB
|
H:ALA9
|
5.0
|
31.1
|
1.0
|
|
Iron binding site 9 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 9 out
of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe401
b:34.3
occ:0.40
|
NE2
|
I:HIS88
|
2.2
|
34.9
|
1.0
|
O
|
I:HOH621
|
2.2
|
53.9
|
1.0
|
OE2
|
I:GLU116
|
2.3
|
40.6
|
1.0
|
NE2
|
I:HIS92
|
2.4
|
52.3
|
1.0
|
O
|
I:HOH680
|
2.4
|
54.5
|
1.0
|
OE1
|
I:GLU116
|
2.6
|
38.3
|
1.0
|
CD
|
I:GLU116
|
2.8
|
32.9
|
1.0
|
CE1
|
I:HIS88
|
2.9
|
35.2
|
1.0
|
CD2
|
I:HIS92
|
3.3
|
52.3
|
1.0
|
CD2
|
I:HIS88
|
3.3
|
32.3
|
1.0
|
CE1
|
I:HIS92
|
3.4
|
54.4
|
1.0
|
O
|
I:HOH522
|
4.0
|
29.4
|
1.0
|
ND1
|
I:HIS88
|
4.1
|
39.0
|
1.0
|
O
|
I:HOH698
|
4.2
|
56.5
|
1.0
|
CG
|
I:GLU116
|
4.3
|
28.4
|
1.0
|
CG
|
I:HIS88
|
4.3
|
35.0
|
1.0
|
OG1
|
I:THR80
|
4.4
|
25.7
|
1.0
|
CG
|
I:HIS92
|
4.4
|
46.7
|
1.0
|
ND1
|
I:HIS92
|
4.4
|
52.4
|
1.0
|
CA
|
I:GLY208
|
4.5
|
34.4
|
1.0
|
CE
|
I:MET91
|
4.8
|
43.6
|
1.0
|
ND2
|
I:ASN11
|
4.8
|
50.4
|
1.0
|
CB
|
I:ALA9
|
4.9
|
26.5
|
1.0
|
|
Iron binding site 10 out
of 24 in 6qpa
Go back to
Iron Binding Sites List in 6qpa
Iron binding site 10 out
of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe401
b:47.8
occ:0.40
|
O
|
J:HOH646
|
2.0
|
50.9
|
1.0
|
OE2
|
J:GLU116
|
2.2
|
51.5
|
1.0
|
NE2
|
J:HIS88
|
2.4
|
46.4
|
1.0
|
NE2
|
J:HIS92
|
2.4
|
55.3
|
1.0
|
O
|
J:HOH687
|
2.8
|
69.7
|
1.0
|
OE1
|
J:GLU116
|
2.8
|
48.9
|
1.0
|
CD
|
J:GLU116
|
2.8
|
42.5
|
1.0
|
CE1
|
J:HIS88
|
3.1
|
42.5
|
1.0
|
CE1
|
J:HIS92
|
3.3
|
57.8
|
1.0
|
CD2
|
J:HIS92
|
3.5
|
55.5
|
1.0
|
CD2
|
J:HIS88
|
3.6
|
42.1
|
1.0
|
O
|
J:HOH513
|
3.7
|
36.3
|
1.0
|
ND1
|
J:HIS88
|
4.3
|
47.3
|
1.0
|
CG
|
J:GLU116
|
4.3
|
39.2
|
1.0
|
OG1
|
J:THR80
|
4.4
|
34.4
|
1.0
|
ND1
|
J:HIS92
|
4.5
|
53.7
|
1.0
|
CG
|
J:HIS92
|
4.6
|
47.5
|
1.0
|
CG
|
J:HIS88
|
4.6
|
45.2
|
1.0
|
CA
|
J:GLY208
|
4.6
|
33.1
|
1.0
|
ND2
|
J:ASN11
|
4.7
|
54.1
|
1.0
|
CE
|
J:MET91
|
4.9
|
55.0
|
1.0
|
|
Reference:
C.Frazao,
A.Klezin,
U.Poell,
A.Veith,
P.Ruehl,
R.Coelho.
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 08:12:28 2024
|