Iron in PDB 1zxi: Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Enzymatic activity of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
All present enzymatic activity of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans:
1.2.99.2;
Protein crystallography data
The structure of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans, PDB code: 1zxi
was solved by
M.Resch,
H.Dobbek,
O.Meyer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.840,
131.320,
159.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.6 /
19.4
|
Other elements in 1zxi:
The structure of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
(pdb code 1zxi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans, PDB code: 1zxi:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 1 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3907
b:9.6
occ:1.00
|
FE1
|
A:FES3907
|
0.0
|
9.6
|
1.0
|
S2
|
A:FES3907
|
2.2
|
8.1
|
1.0
|
S1
|
A:FES3907
|
2.2
|
7.3
|
1.0
|
SG
|
A:CYS102
|
2.3
|
8.8
|
1.0
|
SG
|
A:CYS139
|
2.4
|
8.7
|
1.0
|
FE2
|
A:FES3907
|
2.7
|
9.2
|
1.0
|
CB
|
A:CYS139
|
3.3
|
9.6
|
1.0
|
CB
|
A:CYS102
|
3.5
|
8.4
|
1.0
|
N
|
A:CYS102
|
3.6
|
9.0
|
1.0
|
N
|
A:GLY103
|
3.9
|
9.6
|
1.0
|
O
|
B:HOH3936
|
3.9
|
11.5
|
1.0
|
CA
|
A:CYS102
|
3.9
|
8.5
|
1.0
|
N
|
A:CYS139
|
4.0
|
9.8
|
1.0
|
N
|
A:TYR104
|
4.2
|
10.7
|
1.0
|
CA
|
A:CYS139
|
4.3
|
10.1
|
1.0
|
C
|
A:CYS102
|
4.3
|
9.0
|
1.0
|
SG
|
A:CYS137
|
4.4
|
8.8
|
1.0
|
C
|
A:GLN101
|
4.7
|
8.6
|
1.0
|
N
|
A:CYS105
|
4.7
|
11.8
|
1.0
|
N
|
A:ARG138
|
4.7
|
9.8
|
1.0
|
SG
|
A:CYS105
|
4.7
|
12.1
|
1.0
|
CB
|
A:TYR104
|
4.8
|
9.5
|
1.0
|
N
|
A:GLN101
|
4.8
|
7.1
|
1.0
|
CA
|
A:GLY103
|
4.9
|
11.4
|
1.0
|
CA
|
A:TYR104
|
5.0
|
10.5
|
1.0
|
C
|
A:ARG138
|
5.0
|
10.4
|
1.0
|
CB
|
A:GLN101
|
5.0
|
8.7
|
1.0
|
C
|
A:GLY103
|
5.0
|
11.3
|
1.0
|
|
Iron binding site 2 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 2 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3907
b:9.2
occ:1.00
|
FE2
|
A:FES3907
|
0.0
|
9.2
|
1.0
|
S2
|
A:FES3907
|
2.2
|
8.1
|
1.0
|
S1
|
A:FES3907
|
2.2
|
7.3
|
1.0
|
SG
|
A:CYS105
|
2.3
|
12.1
|
1.0
|
SG
|
A:CYS137
|
2.4
|
8.8
|
1.0
|
FE1
|
A:FES3907
|
2.7
|
9.6
|
1.0
|
CB
|
A:CYS105
|
3.4
|
12.4
|
1.0
|
CB
|
A:CYS137
|
3.4
|
8.6
|
1.0
|
CA
|
A:CYS137
|
3.8
|
8.9
|
1.0
|
N
|
A:CYS105
|
4.0
|
11.8
|
1.0
|
N
|
A:ARG138
|
4.1
|
9.8
|
1.0
|
N
|
A:CYS139
|
4.2
|
9.8
|
1.0
|
CA
|
A:CYS105
|
4.3
|
10.9
|
1.0
|
O
|
A:HOH3911
|
4.3
|
10.3
|
1.0
|
C
|
A:CYS137
|
4.4
|
10.3
|
1.0
|
CB
|
A:CYS139
|
4.4
|
9.6
|
1.0
|
SG
|
A:CYS139
|
4.5
|
8.7
|
1.0
|
SG
|
A:CYS102
|
4.7
|
8.8
|
1.0
|
CG2
|
A:THR140
|
4.7
|
11.6
|
1.0
|
CA
|
A:CYS139
|
4.9
|
10.1
|
1.0
|
C
|
A:CYS105
|
4.9
|
11.1
|
1.0
|
N
|
A:THR106
|
5.0
|
11.1
|
1.0
|
N
|
A:THR140
|
5.0
|
9.7
|
1.0
|
|
Iron binding site 3 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 3 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3908
b:13.1
occ:1.00
|
FE1
|
A:FES3908
|
0.0
|
13.1
|
1.0
|
S2
|
A:FES3908
|
2.3
|
10.3
|
1.0
|
S1
|
A:FES3908
|
2.3
|
13.2
|
1.0
|
SG
|
A:CYS47
|
2.3
|
10.4
|
1.0
|
SG
|
A:CYS42
|
2.4
|
11.5
|
1.0
|
FE2
|
A:FES3908
|
2.7
|
10.4
|
1.0
|
CB
|
A:CYS47
|
3.5
|
9.1
|
1.0
|
N
|
A:CYS47
|
3.5
|
10.3
|
1.0
|
N
|
A:CYS42
|
3.5
|
11.3
|
1.0
|
CB
|
A:CYS42
|
3.6
|
11.3
|
1.0
|
N
|
A:GLY48
|
3.8
|
9.4
|
1.0
|
CA
|
A:CYS47
|
3.8
|
9.8
|
1.0
|
O
|
A:HOH3954
|
3.9
|
20.9
|
1.0
|
CA
|
A:CYS42
|
4.0
|
10.7
|
1.0
|
O
|
A:CYS42
|
4.0
|
10.4
|
1.0
|
N
|
A:GLY41
|
4.1
|
9.8
|
1.0
|
C
|
A:GLY41
|
4.2
|
11.6
|
1.0
|
C
|
A:CYS42
|
4.2
|
11.2
|
1.0
|
C
|
A:CYS47
|
4.2
|
10.1
|
1.0
|
SG
|
A:CYS62
|
4.4
|
11.7
|
1.0
|
N
|
A:HIS46
|
4.4
|
11.0
|
1.0
|
CA
|
A:GLY41
|
4.5
|
10.9
|
1.0
|
N
|
A:ALA49
|
4.6
|
9.1
|
1.0
|
C
|
A:HIS46
|
4.6
|
11.2
|
1.0
|
CA
|
A:SER45
|
4.6
|
11.1
|
1.0
|
SG
|
A:CYS50
|
4.7
|
10.6
|
1.0
|
C
|
A:SER45
|
4.7
|
10.6
|
1.0
|
N
|
A:SER45
|
4.7
|
11.1
|
1.0
|
CA
|
A:GLY48
|
4.8
|
10.8
|
1.0
|
O
|
A:GLY41
|
5.0
|
10.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 4 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3908
b:10.4
occ:1.00
|
FE2
|
A:FES3908
|
0.0
|
10.4
|
1.0
|
S2
|
A:FES3908
|
2.2
|
10.3
|
1.0
|
S1
|
A:FES3908
|
2.2
|
13.2
|
1.0
|
SG
|
A:CYS50
|
2.3
|
10.6
|
1.0
|
SG
|
A:CYS62
|
2.4
|
11.7
|
1.0
|
FE1
|
A:FES3908
|
2.7
|
13.1
|
1.0
|
CB
|
A:CYS62
|
3.2
|
10.6
|
1.0
|
CB
|
A:CYS50
|
3.4
|
9.7
|
1.0
|
O
|
A:HOH3954
|
3.9
|
20.9
|
1.0
|
N
|
A:CYS50
|
4.3
|
8.3
|
1.0
|
N
|
A:CYS62
|
4.3
|
9.6
|
1.0
|
CA
|
A:CYS62
|
4.4
|
9.3
|
1.0
|
CB
|
A:LYS60
|
4.4
|
9.6
|
1.0
|
SG
|
A:CYS47
|
4.4
|
10.4
|
1.0
|
CA
|
A:CYS50
|
4.5
|
9.4
|
1.0
|
N
|
A:GLY48
|
4.5
|
9.4
|
1.0
|
SG
|
A:CYS42
|
4.6
|
11.5
|
1.0
|
CA
|
A:SER45
|
4.8
|
11.1
|
1.0
|
N
|
A:ALA49
|
4.8
|
9.1
|
1.0
|
CA
|
A:GLY48
|
4.9
|
10.8
|
1.0
|
CG
|
A:LYS60
|
4.9
|
9.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 5 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3907
b:8.0
occ:1.00
|
FE1
|
D:FES3907
|
0.0
|
8.0
|
1.0
|
S2
|
D:FES3907
|
2.2
|
11.6
|
1.0
|
S1
|
D:FES3907
|
2.2
|
11.9
|
1.0
|
SG
|
D:CYS102
|
2.3
|
6.4
|
1.0
|
SG
|
D:CYS139
|
2.4
|
10.6
|
1.0
|
FE2
|
D:FES3907
|
2.7
|
8.8
|
1.0
|
CB
|
D:CYS139
|
3.4
|
7.7
|
1.0
|
CB
|
D:CYS102
|
3.4
|
8.5
|
1.0
|
N
|
D:CYS102
|
3.5
|
8.8
|
1.0
|
CA
|
D:CYS102
|
3.9
|
7.8
|
1.0
|
N
|
D:GLY103
|
3.9
|
10.3
|
1.0
|
O
|
E:HOH3931
|
3.9
|
11.4
|
1.0
|
N
|
D:CYS139
|
4.0
|
9.9
|
1.0
|
N
|
D:TYR104
|
4.2
|
10.1
|
1.0
|
C
|
D:CYS102
|
4.2
|
8.6
|
1.0
|
CA
|
D:CYS139
|
4.3
|
10.1
|
1.0
|
SG
|
D:CYS137
|
4.4
|
10.2
|
1.0
|
C
|
D:GLN101
|
4.6
|
8.7
|
1.0
|
N
|
D:CYS105
|
4.7
|
9.0
|
1.0
|
N
|
D:ARG138
|
4.7
|
8.8
|
1.0
|
CB
|
D:TYR104
|
4.7
|
10.6
|
1.0
|
SG
|
D:CYS105
|
4.8
|
12.1
|
1.0
|
N
|
D:GLN101
|
4.8
|
9.7
|
1.0
|
CA
|
D:GLY103
|
4.9
|
9.4
|
1.0
|
CA
|
D:TYR104
|
4.9
|
9.7
|
1.0
|
C
|
D:GLY103
|
5.0
|
9.9
|
1.0
|
C
|
D:ARG138
|
5.0
|
8.4
|
1.0
|
CB
|
D:GLN101
|
5.0
|
11.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 6 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3907
b:8.8
occ:1.00
|
FE2
|
D:FES3907
|
0.0
|
8.8
|
1.0
|
S2
|
D:FES3907
|
2.2
|
11.6
|
1.0
|
S1
|
D:FES3907
|
2.2
|
11.9
|
1.0
|
SG
|
D:CYS105
|
2.3
|
12.1
|
1.0
|
SG
|
D:CYS137
|
2.4
|
10.2
|
1.0
|
FE1
|
D:FES3907
|
2.7
|
8.0
|
1.0
|
CB
|
D:CYS105
|
3.4
|
7.7
|
1.0
|
CB
|
D:CYS137
|
3.5
|
7.5
|
1.0
|
CA
|
D:CYS137
|
3.7
|
8.4
|
1.0
|
N
|
D:CYS105
|
4.0
|
9.0
|
1.0
|
N
|
D:ARG138
|
4.0
|
8.8
|
1.0
|
N
|
D:CYS139
|
4.2
|
9.9
|
1.0
|
CA
|
D:CYS105
|
4.3
|
8.6
|
1.0
|
C
|
D:CYS137
|
4.3
|
8.9
|
1.0
|
CB
|
D:CYS139
|
4.4
|
7.7
|
1.0
|
O
|
D:HOH3918
|
4.4
|
9.1
|
1.0
|
SG
|
D:CYS139
|
4.5
|
10.6
|
1.0
|
SG
|
D:CYS102
|
4.7
|
6.4
|
1.0
|
CG2
|
D:THR140
|
4.8
|
9.7
|
1.0
|
C
|
D:CYS105
|
4.9
|
9.5
|
1.0
|
CA
|
D:CYS139
|
4.9
|
10.1
|
1.0
|
N
|
D:THR106
|
4.9
|
10.0
|
1.0
|
O
|
D:LEU136
|
5.0
|
10.6
|
1.0
|
|
Iron binding site 7 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 7 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3908
b:10.1
occ:1.00
|
FE1
|
D:FES3908
|
0.0
|
10.1
|
1.0
|
S2
|
D:FES3908
|
2.3
|
10.5
|
1.0
|
S1
|
D:FES3908
|
2.3
|
11.1
|
1.0
|
SG
|
D:CYS42
|
2.3
|
10.6
|
1.0
|
SG
|
D:CYS47
|
2.3
|
10.3
|
1.0
|
FE2
|
D:FES3908
|
2.7
|
9.7
|
1.0
|
CB
|
D:CYS47
|
3.5
|
10.2
|
1.0
|
N
|
D:CYS42
|
3.5
|
10.5
|
1.0
|
CB
|
D:CYS42
|
3.5
|
10.7
|
1.0
|
N
|
D:CYS47
|
3.5
|
10.0
|
1.0
|
N
|
D:GLY48
|
3.8
|
10.1
|
1.0
|
CA
|
D:CYS47
|
3.8
|
10.2
|
1.0
|
CA
|
D:CYS42
|
3.9
|
9.2
|
1.0
|
O
|
D:CYS42
|
4.0
|
10.7
|
1.0
|
O
|
D:HOH3964
|
4.1
|
16.0
|
1.0
|
N
|
D:GLY41
|
4.1
|
9.7
|
1.0
|
C
|
D:CYS42
|
4.2
|
10.3
|
1.0
|
C
|
D:GLY41
|
4.2
|
10.4
|
1.0
|
C
|
D:CYS47
|
4.2
|
9.8
|
1.0
|
SG
|
D:CYS62
|
4.4
|
10.0
|
1.0
|
N
|
D:HIS46
|
4.4
|
9.8
|
1.0
|
CA
|
D:GLY41
|
4.5
|
10.5
|
1.0
|
N
|
D:ALA49
|
4.6
|
9.3
|
1.0
|
C
|
D:HIS46
|
4.6
|
10.2
|
1.0
|
CA
|
D:SER45
|
4.6
|
9.7
|
1.0
|
C
|
D:SER45
|
4.7
|
10.8
|
1.0
|
N
|
D:SER45
|
4.7
|
9.8
|
1.0
|
SG
|
D:CYS50
|
4.7
|
8.6
|
1.0
|
CA
|
D:GLY48
|
4.8
|
9.0
|
1.0
|
|
Iron binding site 8 out
of 8 in 1zxi
Go back to
Iron Binding Sites List in 1zxi
Iron binding site 8 out
of 8 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3908
b:9.7
occ:1.00
|
FE2
|
D:FES3908
|
0.0
|
9.7
|
1.0
|
S2
|
D:FES3908
|
2.2
|
10.5
|
1.0
|
S1
|
D:FES3908
|
2.2
|
11.1
|
1.0
|
SG
|
D:CYS50
|
2.3
|
8.6
|
1.0
|
SG
|
D:CYS62
|
2.4
|
10.0
|
1.0
|
FE1
|
D:FES3908
|
2.7
|
10.1
|
1.0
|
CB
|
D:CYS62
|
3.2
|
8.0
|
1.0
|
CB
|
D:CYS50
|
3.4
|
8.9
|
1.0
|
O
|
D:HOH3964
|
4.0
|
16.0
|
1.0
|
N
|
D:CYS50
|
4.3
|
9.7
|
1.0
|
N
|
D:CYS62
|
4.3
|
9.2
|
1.0
|
CA
|
D:CYS62
|
4.4
|
9.3
|
1.0
|
CB
|
D:LYS60
|
4.4
|
10.8
|
1.0
|
CA
|
D:CYS50
|
4.5
|
9.1
|
1.0
|
SG
|
D:CYS47
|
4.5
|
10.3
|
1.0
|
SG
|
D:CYS42
|
4.5
|
10.6
|
1.0
|
N
|
D:GLY48
|
4.6
|
10.1
|
1.0
|
CG
|
D:LYS60
|
4.8
|
10.5
|
1.0
|
CA
|
D:SER45
|
4.8
|
9.7
|
1.0
|
CA
|
D:GLY48
|
4.9
|
9.0
|
1.0
|
N
|
D:ALA49
|
4.9
|
9.3
|
1.0
|
|
Reference:
M.Resch,
H.Dobbek,
O.Meyer.
Structural and Functional Reconstruction in Situ of the [Cusmoo(2)] Active Site of Carbon Monoxide Dehydrogenase From the Carbon Monoxide Oxidizing Eubacterium Oligotropha Carboxidovorans J.Biol.Inorg.Chem. V. 10 518 2005.
ISSN: ISSN 0949-8257
PubMed: 16091936
DOI: 10.1007/S00775-005-0006-4
Page generated: Sat Aug 3 18:43:33 2024
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