Iron in PDB 2yav: Zn Inhibited Sulfur Oxygenase Reductase
Enzymatic activity of Zn Inhibited Sulfur Oxygenase Reductase
All present enzymatic activity of Zn Inhibited Sulfur Oxygenase Reductase:
1.13.11.55;
Protein crystallography data
The structure of Zn Inhibited Sulfur Oxygenase Reductase, PDB code: 2yav
was solved by
A.Veith,
T.Urich,
K.Seyfarth,
J.Protze,
C.Frazao,
A.Kletzin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.20 /
1.70
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
162.074,
162.074,
154.237,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.4 /
19.3
|
Other elements in 2yav:
The structure of Zn Inhibited Sulfur Oxygenase Reductase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Zn Inhibited Sulfur Oxygenase Reductase
(pdb code 2yav). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Zn Inhibited Sulfur Oxygenase Reductase, PDB code: 2yav:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 1 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:15.4
occ:1.00
|
NE2
|
A:HIS86
|
2.0
|
18.6
|
1.0
|
O
|
A:HOH2074
|
2.1
|
19.7
|
1.0
|
NE2
|
A:HIS90
|
2.1
|
23.0
|
1.0
|
OE2
|
A:GLU114
|
2.2
|
17.5
|
1.0
|
OE1
|
A:GLU114
|
2.3
|
17.3
|
1.0
|
O
|
A:HOH2006
|
2.3
|
21.5
|
1.0
|
CD
|
A:GLU114
|
2.5
|
14.5
|
1.0
|
CE1
|
A:HIS86
|
3.0
|
19.2
|
1.0
|
CD2
|
A:HIS86
|
3.1
|
18.6
|
1.0
|
CE1
|
A:HIS90
|
3.1
|
28.2
|
1.0
|
CD2
|
A:HIS90
|
3.2
|
22.4
|
1.0
|
O
|
A:HOH2096
|
4.0
|
16.1
|
1.0
|
CG
|
A:GLU114
|
4.1
|
15.1
|
1.0
|
ND1
|
A:HIS86
|
4.1
|
18.0
|
1.0
|
CG
|
A:HIS86
|
4.2
|
16.4
|
1.0
|
ND1
|
A:HIS90
|
4.2
|
25.1
|
1.0
|
CG
|
A:HIS90
|
4.3
|
22.2
|
1.0
|
ND2
|
A:ASN9
|
4.3
|
31.7
|
1.0
|
O
|
A:HOH2004
|
4.6
|
41.4
|
1.0
|
OG1
|
A:THR78
|
4.7
|
13.2
|
1.0
|
CA
|
A:GLY208
|
4.7
|
18.6
|
1.0
|
CB
|
A:ALA7
|
4.7
|
15.4
|
1.0
|
CE
|
A:MET89
|
4.7
|
24.9
|
1.0
|
CB
|
A:GLU114
|
5.0
|
15.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 2 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:15.4
occ:1.00
|
NE2
|
B:HIS86
|
2.1
|
13.2
|
1.0
|
NE2
|
B:HIS90
|
2.1
|
21.4
|
1.0
|
O
|
B:HOH2063
|
2.1
|
22.4
|
1.0
|
OE2
|
B:GLU114
|
2.2
|
15.8
|
1.0
|
OE1
|
B:GLU114
|
2.2
|
17.8
|
1.0
|
O
|
B:HOH2007
|
2.2
|
19.8
|
1.0
|
CD
|
B:GLU114
|
2.5
|
17.8
|
1.0
|
CE1
|
B:HIS86
|
3.0
|
20.5
|
1.0
|
CE1
|
B:HIS90
|
3.1
|
25.0
|
1.0
|
CD2
|
B:HIS86
|
3.1
|
14.8
|
1.0
|
CD2
|
B:HIS90
|
3.2
|
18.0
|
1.0
|
O
|
B:HOH2085
|
4.0
|
14.2
|
1.0
|
CG
|
B:GLU114
|
4.0
|
14.5
|
1.0
|
ND1
|
B:HIS86
|
4.2
|
17.7
|
1.0
|
ND1
|
B:HIS90
|
4.2
|
22.6
|
1.0
|
CG
|
B:HIS86
|
4.2
|
13.8
|
1.0
|
ND2
|
B:ASN9
|
4.3
|
39.7
|
1.0
|
CG
|
B:HIS90
|
4.3
|
20.2
|
1.0
|
O
|
B:HOH2005
|
4.6
|
45.5
|
1.0
|
CA
|
B:GLY208
|
4.6
|
14.0
|
1.0
|
CB
|
B:ALA7
|
4.7
|
14.2
|
1.0
|
OG1
|
B:THR78
|
4.7
|
13.8
|
1.0
|
CE
|
B:MET89
|
4.8
|
24.5
|
1.0
|
CB
|
B:GLU114
|
4.9
|
15.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 3 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:15.6
occ:1.00
|
O
|
C:HOH2063
|
2.1
|
19.9
|
1.0
|
NE2
|
C:HIS86
|
2.1
|
16.2
|
1.0
|
NE2
|
C:HIS90
|
2.1
|
24.7
|
1.0
|
OE2
|
C:GLU114
|
2.2
|
18.2
|
1.0
|
O
|
C:HOH2005
|
2.2
|
22.5
|
1.0
|
OE1
|
C:GLU114
|
2.3
|
14.5
|
1.0
|
CD
|
C:GLU114
|
2.6
|
14.0
|
1.0
|
CE1
|
C:HIS86
|
3.0
|
16.4
|
1.0
|
CE1
|
C:HIS90
|
3.0
|
21.3
|
1.0
|
CD2
|
C:HIS86
|
3.1
|
17.1
|
1.0
|
CD2
|
C:HIS90
|
3.1
|
23.9
|
1.0
|
O
|
C:HOH2088
|
4.0
|
15.2
|
1.0
|
CG
|
C:GLU114
|
4.1
|
12.1
|
1.0
|
ND1
|
C:HIS86
|
4.2
|
18.6
|
1.0
|
ND1
|
C:HIS90
|
4.2
|
23.5
|
1.0
|
CG
|
C:HIS86
|
4.2
|
13.2
|
1.0
|
ND2
|
C:ASN9
|
4.3
|
34.0
|
1.0
|
CG
|
C:HIS90
|
4.3
|
23.4
|
1.0
|
O
|
C:HOH2003
|
4.6
|
47.0
|
1.0
|
CA
|
C:GLY208
|
4.7
|
16.4
|
1.0
|
OG1
|
C:THR78
|
4.7
|
15.6
|
1.0
|
CE
|
C:MET89
|
4.7
|
26.9
|
1.0
|
CB
|
C:ALA7
|
4.8
|
13.3
|
1.0
|
CB
|
C:GLU114
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 4 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe402
b:15.7
occ:1.00
|
O
|
D:HOH2070
|
2.0
|
19.2
|
1.0
|
NE2
|
D:HIS86
|
2.1
|
14.0
|
1.0
|
NE2
|
D:HIS90
|
2.2
|
23.8
|
1.0
|
OE2
|
D:GLU114
|
2.2
|
15.5
|
1.0
|
O
|
D:HOH2007
|
2.2
|
20.5
|
1.0
|
OE1
|
D:GLU114
|
2.3
|
16.5
|
1.0
|
CD
|
D:GLU114
|
2.6
|
13.7
|
1.0
|
CE1
|
D:HIS86
|
3.1
|
18.0
|
1.0
|
CD2
|
D:HIS86
|
3.1
|
15.8
|
1.0
|
CE1
|
D:HIS90
|
3.1
|
26.0
|
1.0
|
CD2
|
D:HIS90
|
3.2
|
21.2
|
1.0
|
O
|
D:HOH2015
|
3.9
|
42.5
|
1.0
|
O
|
D:HOH2092
|
3.9
|
17.6
|
1.0
|
CG
|
D:GLU114
|
4.1
|
14.9
|
1.0
|
ND1
|
D:HIS86
|
4.2
|
16.0
|
1.0
|
CG
|
D:HIS86
|
4.2
|
17.0
|
1.0
|
ND1
|
D:HIS90
|
4.2
|
24.9
|
1.0
|
ND2
|
D:ASN9
|
4.3
|
36.0
|
1.0
|
CG
|
D:HIS90
|
4.3
|
19.8
|
1.0
|
O
|
D:HOH2005
|
4.4
|
44.7
|
1.0
|
OG1
|
D:THR78
|
4.7
|
14.2
|
1.0
|
CE
|
D:MET89
|
4.7
|
25.5
|
1.0
|
CA
|
D:GLY208
|
4.7
|
15.6
|
1.0
|
CB
|
D:ALA7
|
4.7
|
14.0
|
1.0
|
CB
|
D:GLU114
|
5.0
|
14.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 5 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe402
b:14.8
occ:1.00
|
NE2
|
E:HIS86
|
2.1
|
14.9
|
1.0
|
OE2
|
E:GLU114
|
2.1
|
13.7
|
1.0
|
NE2
|
E:HIS90
|
2.2
|
23.3
|
1.0
|
O
|
E:HOH2003
|
2.2
|
18.9
|
1.0
|
O
|
E:HOH2056
|
2.2
|
18.9
|
1.0
|
OE1
|
E:GLU114
|
2.3
|
15.0
|
1.0
|
CD
|
E:GLU114
|
2.5
|
13.1
|
1.0
|
CE1
|
E:HIS86
|
3.0
|
17.6
|
1.0
|
CD2
|
E:HIS86
|
3.1
|
16.7
|
1.0
|
CE1
|
E:HIS90
|
3.1
|
24.1
|
1.0
|
CD2
|
E:HIS90
|
3.2
|
21.2
|
1.0
|
O
|
E:HOH2077
|
3.9
|
14.2
|
1.0
|
CG
|
E:GLU114
|
4.0
|
14.9
|
1.0
|
O
|
E:HOH2013
|
4.1
|
37.8
|
1.0
|
ND1
|
E:HIS86
|
4.2
|
16.3
|
1.0
|
CG
|
E:HIS86
|
4.2
|
14.8
|
1.0
|
ND2
|
E:ASN9
|
4.3
|
34.0
|
1.0
|
ND1
|
E:HIS90
|
4.3
|
20.5
|
1.0
|
CG
|
E:HIS90
|
4.3
|
20.5
|
1.0
|
O
|
E:HOH2002
|
4.4
|
40.2
|
1.0
|
CA
|
E:GLY208
|
4.6
|
17.2
|
1.0
|
CB
|
E:ALA7
|
4.7
|
12.9
|
1.0
|
OG1
|
E:THR78
|
4.7
|
15.0
|
1.0
|
CE
|
E:MET89
|
4.8
|
24.8
|
1.0
|
CB
|
E:GLU114
|
4.9
|
12.7
|
1.0
|
O
|
E:HOH2006
|
4.9
|
46.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 2yav
Go back to
Iron Binding Sites List in 2yav
Iron binding site 6 out
of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe402
b:15.1
occ:1.00
|
NE2
|
F:HIS90
|
2.1
|
19.6
|
1.0
|
O
|
F:HOH2009
|
2.1
|
20.2
|
1.0
|
NE2
|
F:HIS86
|
2.2
|
15.9
|
1.0
|
OE2
|
F:GLU114
|
2.2
|
16.2
|
1.0
|
OE1
|
F:GLU114
|
2.2
|
14.2
|
1.0
|
O
|
F:HOH2080
|
2.3
|
20.6
|
1.0
|
CD
|
F:GLU114
|
2.5
|
13.3
|
1.0
|
CE1
|
F:HIS90
|
3.0
|
24.3
|
1.0
|
CE1
|
F:HIS86
|
3.1
|
15.8
|
1.0
|
CD2
|
F:HIS86
|
3.2
|
16.1
|
1.0
|
CD2
|
F:HIS90
|
3.2
|
20.0
|
1.0
|
CG
|
F:GLU114
|
4.0
|
12.7
|
1.0
|
O
|
F:HOH2106
|
4.1
|
14.1
|
1.0
|
ND1
|
F:HIS90
|
4.2
|
23.1
|
1.0
|
ND1
|
F:HIS86
|
4.2
|
15.7
|
1.0
|
ND2
|
F:ASN9
|
4.2
|
36.8
|
1.0
|
CG
|
F:HIS90
|
4.3
|
22.5
|
1.0
|
CG
|
F:HIS86
|
4.3
|
13.6
|
1.0
|
O
|
F:HOH2007
|
4.4
|
42.0
|
1.0
|
CA
|
F:GLY208
|
4.6
|
17.8
|
1.0
|
CE
|
F:MET89
|
4.8
|
28.8
|
1.0
|
CB
|
F:ALA7
|
4.8
|
12.1
|
1.0
|
OG1
|
F:THR78
|
4.8
|
12.8
|
1.0
|
CB
|
F:GLU114
|
4.9
|
14.8
|
1.0
|
|
Reference:
A.Veith,
T.Urich,
K.Seyfarth,
J.Protze,
C.Frazao,
A.Kletzin.
Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens. Front.Microbiol. V. 2 37 2011.
ISSN: ESSN 1664-302X
PubMed: 21747782
DOI: 10.3389/FMICB.2011.00037
Page generated: Sun Aug 4 05:11:12 2024
|