Iron in PDB 1ffu: Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Protein crystallography data
The structure of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor, PDB code: 1ffu
was solved by
P.Haenzelmann,
H.Dobbek,
L.Gremer,
R.Huber,
O.Meyer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.35
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.235,
193.884,
218.290,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
24.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
(pdb code 1ffu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor, PDB code: 1ffu:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 1 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1907
b:24.1
occ:1.00
|
FE1
|
A:FES1907
|
0.0
|
24.1
|
1.0
|
S1
|
A:FES1907
|
2.2
|
25.0
|
1.0
|
S2
|
A:FES1907
|
2.2
|
25.1
|
1.0
|
SG
|
A:CYS101
|
2.3
|
25.2
|
1.0
|
SG
|
A:CYS138
|
2.4
|
25.8
|
1.0
|
FE2
|
A:FES1907
|
2.7
|
26.1
|
1.0
|
CB
|
A:CYS101
|
3.3
|
25.8
|
1.0
|
CB
|
A:CYS138
|
3.5
|
25.4
|
1.0
|
N
|
A:CYS101
|
3.7
|
25.5
|
1.0
|
O
|
B:HOH1925
|
3.7
|
25.9
|
1.0
|
CA
|
A:CYS101
|
3.9
|
25.6
|
1.0
|
N
|
A:GLY102
|
4.0
|
25.6
|
1.0
|
N
|
A:CYS138
|
4.1
|
24.8
|
1.0
|
N
|
A:PHE103
|
4.2
|
24.7
|
1.0
|
C
|
A:CYS101
|
4.3
|
26.0
|
1.0
|
SG
|
A:CYS136
|
4.3
|
23.7
|
1.0
|
CA
|
A:CYS138
|
4.4
|
25.5
|
1.0
|
CB
|
A:PHE103
|
4.7
|
23.5
|
1.0
|
N
|
A:ARG137
|
4.7
|
24.4
|
1.0
|
SG
|
A:CYS104
|
4.7
|
25.3
|
1.0
|
N
|
A:CYS104
|
4.8
|
24.0
|
1.0
|
C
|
A:GLN100
|
4.8
|
25.3
|
1.0
|
C
|
A:ARG137
|
4.9
|
24.8
|
1.0
|
CA
|
A:GLY102
|
4.9
|
25.1
|
1.0
|
CA
|
A:PHE103
|
4.9
|
24.1
|
1.0
|
|
Iron binding site 2 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 2 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1907
b:26.1
occ:1.00
|
FE2
|
A:FES1907
|
0.0
|
26.1
|
1.0
|
S1
|
A:FES1907
|
2.2
|
25.0
|
1.0
|
S2
|
A:FES1907
|
2.2
|
25.1
|
1.0
|
SG
|
A:CYS104
|
2.3
|
25.3
|
1.0
|
SG
|
A:CYS136
|
2.3
|
23.7
|
1.0
|
FE1
|
A:FES1907
|
2.7
|
24.1
|
1.0
|
CB
|
A:CYS104
|
3.4
|
24.5
|
1.0
|
CB
|
A:CYS136
|
3.5
|
24.3
|
1.0
|
CA
|
A:CYS136
|
3.8
|
24.3
|
1.0
|
N
|
A:CYS104
|
4.0
|
24.0
|
1.0
|
N
|
A:ARG137
|
4.1
|
24.4
|
1.0
|
CA
|
A:CYS104
|
4.3
|
23.9
|
1.0
|
N
|
A:CYS138
|
4.3
|
24.8
|
1.0
|
O
|
A:HOH1919
|
4.3
|
18.5
|
1.0
|
C
|
A:CYS136
|
4.4
|
24.3
|
1.0
|
SG
|
A:CYS138
|
4.5
|
25.8
|
1.0
|
CB
|
A:CYS138
|
4.6
|
25.4
|
1.0
|
SG
|
A:CYS101
|
4.7
|
25.2
|
1.0
|
CG2
|
A:THR139
|
4.8
|
24.3
|
1.0
|
C
|
A:CYS104
|
4.9
|
23.9
|
1.0
|
N
|
A:THR105
|
4.9
|
24.0
|
1.0
|
O
|
A:LEU135
|
4.9
|
24.9
|
1.0
|
N
|
A:PHE103
|
4.9
|
24.7
|
1.0
|
N
|
A:THR139
|
5.0
|
25.5
|
1.0
|
CA
|
A:CYS138
|
5.0
|
25.5
|
1.0
|
|
Iron binding site 3 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 3 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1908
b:26.1
occ:1.00
|
FE1
|
A:FES1908
|
0.0
|
26.1
|
1.0
|
S1
|
A:FES1908
|
2.2
|
24.6
|
1.0
|
S2
|
A:FES1908
|
2.2
|
25.7
|
1.0
|
SG
|
A:CYS47
|
2.3
|
26.1
|
1.0
|
SG
|
A:CYS42
|
2.3
|
25.1
|
1.0
|
FE2
|
A:FES1908
|
2.7
|
26.3
|
1.0
|
N
|
A:CYS42
|
3.5
|
24.6
|
1.0
|
CB
|
A:CYS47
|
3.5
|
24.9
|
1.0
|
CB
|
A:CYS42
|
3.6
|
25.0
|
1.0
|
N
|
A:CYS47
|
3.6
|
24.8
|
1.0
|
N
|
A:GLY48
|
3.7
|
23.8
|
1.0
|
O
|
A:CYS42
|
3.9
|
25.1
|
1.0
|
CA
|
A:CYS47
|
3.9
|
24.7
|
1.0
|
CA
|
A:CYS42
|
3.9
|
24.7
|
1.0
|
O
|
A:HOH1923
|
3.9
|
33.3
|
1.0
|
C
|
A:CYS42
|
4.1
|
25.0
|
1.0
|
N
|
A:GLY41
|
4.1
|
23.7
|
1.0
|
C
|
A:GLY41
|
4.3
|
24.5
|
1.0
|
C
|
A:CYS47
|
4.3
|
24.2
|
1.0
|
N
|
A:HIS46
|
4.3
|
24.8
|
1.0
|
SG
|
A:CYS62
|
4.3
|
25.0
|
1.0
|
CA
|
A:GLY41
|
4.5
|
24.0
|
1.0
|
CA
|
A:SER45
|
4.5
|
25.0
|
1.0
|
C
|
A:HIS46
|
4.6
|
25.2
|
1.0
|
C
|
A:SER45
|
4.6
|
25.1
|
1.0
|
N
|
A:ALA49
|
4.6
|
24.1
|
1.0
|
N
|
A:SER45
|
4.6
|
25.0
|
1.0
|
SG
|
A:CYS50
|
4.6
|
23.4
|
1.0
|
CA
|
A:GLY48
|
4.7
|
23.4
|
1.0
|
CA
|
A:HIS46
|
5.0
|
24.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 4 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1908
b:26.3
occ:1.00
|
FE2
|
A:FES1908
|
0.0
|
26.3
|
1.0
|
S1
|
A:FES1908
|
2.2
|
24.6
|
1.0
|
S2
|
A:FES1908
|
2.2
|
25.7
|
1.0
|
SG
|
A:CYS50
|
2.3
|
23.4
|
1.0
|
SG
|
A:CYS62
|
2.3
|
25.0
|
1.0
|
FE1
|
A:FES1908
|
2.7
|
26.1
|
1.0
|
CB
|
A:CYS62
|
3.2
|
25.0
|
1.0
|
CB
|
A:CYS50
|
3.4
|
24.5
|
1.0
|
O
|
A:HOH1923
|
3.7
|
33.3
|
1.0
|
N
|
A:CYS62
|
4.3
|
25.1
|
1.0
|
CB
|
A:LYS60
|
4.3
|
24.2
|
1.0
|
N
|
A:CYS50
|
4.4
|
24.3
|
1.0
|
CA
|
A:CYS62
|
4.4
|
24.7
|
1.0
|
SG
|
A:CYS47
|
4.4
|
26.1
|
1.0
|
N
|
A:GLY48
|
4.4
|
23.8
|
1.0
|
CA
|
A:CYS50
|
4.5
|
24.0
|
1.0
|
SG
|
A:CYS42
|
4.6
|
25.1
|
1.0
|
CA
|
A:GLY48
|
4.7
|
23.4
|
1.0
|
CA
|
A:SER45
|
4.7
|
25.0
|
1.0
|
N
|
A:ALA49
|
4.8
|
24.1
|
1.0
|
CG
|
A:LYS60
|
4.9
|
24.3
|
1.0
|
CD
|
A:LYS60
|
4.9
|
24.6
|
1.0
|
O
|
A:CYS42
|
4.9
|
25.1
|
1.0
|
|
Iron binding site 5 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 5 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1909
b:26.1
occ:1.00
|
FE1
|
D:FES1909
|
0.0
|
26.1
|
1.0
|
S1
|
D:FES1909
|
2.2
|
25.6
|
1.0
|
S2
|
D:FES1909
|
2.2
|
25.3
|
1.0
|
SG
|
D:CYS101
|
2.3
|
26.0
|
1.0
|
SG
|
D:CYS138
|
2.4
|
27.5
|
1.0
|
FE2
|
D:FES1909
|
2.7
|
27.0
|
1.0
|
CB
|
D:CYS138
|
3.4
|
27.7
|
1.0
|
CB
|
D:CYS101
|
3.4
|
25.3
|
1.0
|
N
|
D:CYS101
|
3.8
|
25.0
|
1.0
|
O
|
E:HOH1929
|
3.9
|
31.7
|
1.0
|
N
|
D:GLY102
|
3.9
|
24.9
|
1.0
|
N
|
D:CYS138
|
4.0
|
28.0
|
1.0
|
CA
|
D:CYS101
|
4.0
|
24.9
|
1.0
|
N
|
D:PHE103
|
4.2
|
24.4
|
1.0
|
CA
|
D:CYS138
|
4.3
|
27.9
|
1.0
|
C
|
D:CYS101
|
4.3
|
24.6
|
1.0
|
SG
|
D:CYS136
|
4.4
|
25.3
|
1.0
|
N
|
D:ARG137
|
4.7
|
26.7
|
1.0
|
CB
|
D:PHE103
|
4.7
|
23.7
|
1.0
|
N
|
D:CYS104
|
4.8
|
24.7
|
1.0
|
SG
|
D:CYS104
|
4.8
|
25.0
|
1.0
|
CA
|
D:GLY102
|
4.9
|
24.5
|
1.0
|
C
|
D:ARG137
|
4.9
|
27.9
|
1.0
|
C
|
D:GLN100
|
4.9
|
25.6
|
1.0
|
CA
|
D:PHE103
|
4.9
|
24.5
|
1.0
|
|
Iron binding site 6 out
of 8 in 1ffu
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Iron Binding Sites List in 1ffu
Iron binding site 6 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1909
b:27.0
occ:1.00
|
FE2
|
D:FES1909
|
0.0
|
27.0
|
1.0
|
S2
|
D:FES1909
|
2.2
|
25.3
|
1.0
|
S1
|
D:FES1909
|
2.2
|
25.6
|
1.0
|
SG
|
D:CYS104
|
2.3
|
25.0
|
1.0
|
SG
|
D:CYS136
|
2.3
|
25.3
|
1.0
|
FE1
|
D:FES1909
|
2.7
|
26.1
|
1.0
|
CB
|
D:CYS104
|
3.3
|
24.6
|
1.0
|
CB
|
D:CYS136
|
3.5
|
25.8
|
1.0
|
CA
|
D:CYS136
|
3.9
|
25.7
|
1.0
|
N
|
D:CYS104
|
3.9
|
24.7
|
1.0
|
N
|
D:ARG137
|
4.2
|
26.7
|
1.0
|
CA
|
D:CYS104
|
4.2
|
25.1
|
1.0
|
N
|
D:CYS138
|
4.3
|
28.0
|
1.0
|
O
|
D:HOH1961
|
4.4
|
23.8
|
1.0
|
C
|
D:CYS136
|
4.5
|
26.3
|
1.0
|
SG
|
D:CYS138
|
4.5
|
27.5
|
1.0
|
CB
|
D:CYS138
|
4.5
|
27.7
|
1.0
|
CG2
|
D:THR139
|
4.7
|
27.0
|
1.0
|
SG
|
D:CYS101
|
4.7
|
26.0
|
1.0
|
N
|
D:THR105
|
4.8
|
25.3
|
1.0
|
N
|
D:PHE103
|
4.8
|
24.4
|
1.0
|
C
|
D:CYS104
|
4.8
|
25.4
|
1.0
|
N
|
D:THR139
|
4.9
|
28.0
|
1.0
|
CA
|
D:CYS138
|
5.0
|
27.9
|
1.0
|
OG1
|
D:THR105
|
5.0
|
23.5
|
1.0
|
|
Iron binding site 7 out
of 8 in 1ffu
Go back to
Iron Binding Sites List in 1ffu
Iron binding site 7 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1910
b:27.4
occ:1.00
|
FE1
|
D:FES1910
|
0.0
|
27.4
|
1.0
|
S2
|
D:FES1910
|
2.3
|
26.2
|
1.0
|
S1
|
D:FES1910
|
2.3
|
25.8
|
1.0
|
SG
|
D:CYS47
|
2.3
|
26.1
|
1.0
|
SG
|
D:CYS42
|
2.3
|
24.2
|
1.0
|
FE2
|
D:FES1910
|
2.7
|
26.3
|
1.0
|
CB
|
D:CYS47
|
3.5
|
25.8
|
1.0
|
N
|
D:CYS47
|
3.5
|
25.9
|
1.0
|
N
|
D:CYS42
|
3.5
|
25.8
|
1.0
|
CB
|
D:CYS42
|
3.6
|
25.5
|
1.0
|
N
|
D:GLY48
|
3.7
|
25.8
|
1.0
|
CA
|
D:CYS47
|
3.8
|
25.7
|
1.0
|
O
|
D:CYS42
|
3.9
|
26.9
|
1.0
|
CA
|
D:CYS42
|
4.0
|
25.8
|
1.0
|
C
|
D:CYS42
|
4.2
|
25.9
|
1.0
|
N
|
D:GLY41
|
4.2
|
25.2
|
1.0
|
O
|
F:HOH1938
|
4.2
|
27.7
|
1.0
|
C
|
D:GLY41
|
4.2
|
25.8
|
1.0
|
N
|
D:HIS46
|
4.2
|
26.2
|
1.0
|
C
|
D:CYS47
|
4.2
|
25.7
|
1.0
|
SG
|
D:CYS62
|
4.3
|
26.1
|
1.0
|
CA
|
D:GLY41
|
4.5
|
25.3
|
1.0
|
C
|
D:HIS46
|
4.6
|
26.5
|
1.0
|
CA
|
D:SER45
|
4.6
|
26.4
|
1.0
|
N
|
D:ALA49
|
4.6
|
25.5
|
1.0
|
C
|
D:SER45
|
4.7
|
26.6
|
1.0
|
SG
|
D:CYS50
|
4.7
|
25.4
|
1.0
|
N
|
D:SER45
|
4.7
|
26.7
|
1.0
|
CA
|
D:GLY48
|
4.8
|
25.2
|
1.0
|
CA
|
D:HIS46
|
5.0
|
26.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 1ffu
Go back to
Iron Binding Sites List in 1ffu
Iron binding site 8 out
of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1910
b:26.3
occ:1.00
|
FE2
|
D:FES1910
|
0.0
|
26.3
|
1.0
|
S1
|
D:FES1910
|
2.2
|
25.8
|
1.0
|
S2
|
D:FES1910
|
2.3
|
26.2
|
1.0
|
SG
|
D:CYS50
|
2.3
|
25.4
|
1.0
|
SG
|
D:CYS62
|
2.3
|
26.1
|
1.0
|
FE1
|
D:FES1910
|
2.7
|
27.4
|
1.0
|
CB
|
D:CYS62
|
3.3
|
24.9
|
1.0
|
CB
|
D:CYS50
|
3.4
|
25.5
|
1.0
|
O
|
F:HOH1938
|
4.0
|
27.7
|
1.0
|
CB
|
D:LYS60
|
4.3
|
24.7
|
1.0
|
N
|
D:CYS50
|
4.3
|
25.0
|
1.0
|
N
|
D:CYS62
|
4.3
|
25.0
|
1.0
|
SG
|
D:CYS47
|
4.4
|
26.1
|
1.0
|
CA
|
D:CYS62
|
4.4
|
24.9
|
1.0
|
N
|
D:GLY48
|
4.4
|
25.8
|
1.0
|
CA
|
D:CYS50
|
4.5
|
24.9
|
1.0
|
SG
|
D:CYS42
|
4.6
|
24.2
|
1.0
|
CA
|
D:GLY48
|
4.7
|
25.2
|
1.0
|
CD
|
D:LYS60
|
4.7
|
24.6
|
1.0
|
CA
|
D:SER45
|
4.8
|
26.4
|
1.0
|
CG
|
D:LYS60
|
4.8
|
24.4
|
1.0
|
N
|
D:ALA49
|
4.8
|
25.5
|
1.0
|
CA
|
D:LYS60
|
5.0
|
25.3
|
1.0
|
|
Reference:
P.Hanzelmann,
H.Dobbek,
L.Gremer,
R.Huber,
O.Meyer.
The Effect of Intracellular Molybdenum in Hydrogenophaga Pseudoflava on the Crystallographic Structure of the Seleno-Molybdo-Iron-Sulfur Flavoenzyme Carbon Monoxide Dehydrogenase. J.Mol.Biol. V. 301 1221 2000.
ISSN: ISSN 0022-2836
PubMed: 10966817
DOI: 10.1006/JMBI.2000.4023
Page generated: Sat Aug 3 04:59:29 2024
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