Iron in PDB 8ru6: Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
Enzymatic activity of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum:
1.12.7.2;
Protein crystallography data
The structure of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum, PDB code: 8ru6
was solved by
K.Bikbaev,
J.Jaenecke,
M.Winkler,
I.Span,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.75 /
1.15
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.397,
88.857,
106.592,
90,
90,
90
|
|
R / Rfree (%)
|
13.7 /
15.8
|
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Iron atom in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
(pdb code 8ru6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the
Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum, PDB code: 8ru6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 1 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe505
b:10.1
occ:1.00
|
FE1
|
B:SF4505
|
0.0
|
10.1
|
1.0
|
|
S4
|
B:SF4505
|
2.3
|
10.4
|
1.0
|
|
S3
|
B:SF4505
|
2.3
|
10.3
|
1.0
|
|
SG
|
B:CYS45
|
2.3
|
10.5
|
1.0
|
|
S2
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
FE2
|
B:SF4505
|
2.7
|
10.2
|
1.0
|
|
FE4
|
B:SF4505
|
2.7
|
9.8
|
1.0
|
|
FE3
|
B:SF4505
|
2.8
|
9.7
|
1.0
|
|
HG
|
B:CYS45
|
2.8
|
10.3
|
0.0
|
|
HD2
|
B:PRO46
|
3.0
|
11.1
|
1.0
|
|
HB2
|
B:CYS45
|
3.2
|
10.3
|
1.0
|
|
CB
|
B:CYS45
|
3.3
|
10.2
|
1.0
|
|
HA
|
B:CYS45
|
3.3
|
10.4
|
1.0
|
|
HB2
|
B:ALA49
|
3.3
|
11.6
|
1.0
|
|
HD12
|
B:ILE50
|
3.6
|
13.8
|
1.0
|
|
HG13
|
B:ILE50
|
3.6
|
13.1
|
1.0
|
|
CA
|
B:CYS45
|
3.8
|
10.2
|
1.0
|
|
S1
|
B:SF4505
|
3.9
|
9.8
|
1.0
|
|
CD
|
B:PRO46
|
3.9
|
11.2
|
1.0
|
|
HG1
|
B:THR47
|
3.9
|
12.6
|
0.0
|
|
HB3
|
B:CYS45
|
4.1
|
10.3
|
1.0
|
|
H
|
B:ALA49
|
4.2
|
11.3
|
1.0
|
|
HD3
|
B:PRO46
|
4.3
|
11.1
|
1.0
|
|
CB
|
B:ALA49
|
4.3
|
11.8
|
1.0
|
|
CG1
|
B:ILE50
|
4.4
|
13.2
|
1.0
|
|
CD1
|
B:ILE50
|
4.4
|
13.9
|
1.0
|
|
H
|
B:THR47
|
4.4
|
11.3
|
1.0
|
|
HA
|
B:CYS66
|
4.4
|
10.8
|
1.0
|
|
HB1
|
B:ALA49
|
4.4
|
11.6
|
1.0
|
|
OG1
|
B:THR47
|
4.5
|
12.9
|
1.0
|
|
HG
|
B:CYS72
|
4.5
|
10.5
|
0.0
|
|
HB3
|
B:CYS72
|
4.5
|
10.9
|
1.0
|
|
HG12
|
B:ILE50
|
4.5
|
13.2
|
1.0
|
|
N
|
B:PRO46
|
4.5
|
10.8
|
1.0
|
|
C
|
B:CYS45
|
4.6
|
11.0
|
1.0
|
|
H
|
B:ILE67
|
4.6
|
8.9
|
1.0
|
|
HD11
|
B:ILE50
|
4.7
|
13.7
|
1.0
|
|
SG
|
B:CYS69
|
4.7
|
9.9
|
1.0
|
|
HG2
|
B:PRO46
|
4.8
|
11.2
|
1.0
|
|
HB3
|
B:ALA49
|
4.8
|
11.6
|
1.0
|
|
SG
|
B:CYS72
|
4.8
|
10.9
|
1.0
|
|
SG
|
B:CYS66
|
4.9
|
10.3
|
1.0
|
|
CG
|
B:PRO46
|
4.9
|
11.0
|
1.0
|
|
N
|
B:CYS45
|
4.9
|
11.3
|
1.0
|
|
H
|
B:CYS72
|
5.0
|
10.8
|
1.0
|
|
N
|
B:ALA49
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 2 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 2 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe505
b:10.2
occ:1.00
|
FE2
|
B:SF4505
|
0.0
|
10.2
|
1.0
|
|
HG
|
B:CYS72
|
2.2
|
10.5
|
0.0
|
|
S3
|
B:SF4505
|
2.3
|
10.3
|
1.0
|
|
S4
|
B:SF4505
|
2.3
|
10.4
|
1.0
|
|
SG
|
B:CYS72
|
2.3
|
10.9
|
1.0
|
|
S1
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
FE1
|
B:SF4505
|
2.7
|
10.1
|
1.0
|
|
FE4
|
B:SF4505
|
2.7
|
9.8
|
1.0
|
|
FE3
|
B:SF4505
|
2.8
|
9.7
|
1.0
|
|
HB3
|
B:CYS72
|
3.1
|
10.9
|
1.0
|
|
HD12
|
B:ILE50
|
3.3
|
13.8
|
1.0
|
|
H
|
B:CYS72
|
3.3
|
10.8
|
1.0
|
|
CB
|
B:CYS72
|
3.3
|
10.9
|
1.0
|
|
HG13
|
B:VAL28
|
3.8
|
12.8
|
1.0
|
|
S2
|
B:SF4505
|
3.9
|
9.8
|
1.0
|
|
HB2
|
B:CYS72
|
4.0
|
11.0
|
1.0
|
|
N
|
B:CYS72
|
4.1
|
10.7
|
1.0
|
|
H
|
B:GLY70
|
4.1
|
9.4
|
1.0
|
|
HD13
|
B:ILE60
|
4.1
|
13.0
|
1.0
|
|
HD12
|
B:ILE60
|
4.1
|
13.0
|
1.0
|
|
CD1
|
B:ILE50
|
4.2
|
13.9
|
1.0
|
|
HA2
|
B:GLY70
|
4.3
|
9.5
|
1.0
|
|
CA
|
B:CYS72
|
4.3
|
11.1
|
1.0
|
|
H
|
B:GLN71
|
4.4
|
10.1
|
1.0
|
|
H
|
B:LEU73
|
4.5
|
11.0
|
1.0
|
|
HG13
|
B:ILE50
|
4.5
|
13.1
|
1.0
|
|
HD13
|
B:ILE50
|
4.6
|
13.8
|
1.0
|
|
CD1
|
B:ILE60
|
4.6
|
13.1
|
1.0
|
|
HB2
|
B:CYS45
|
4.6
|
10.3
|
1.0
|
|
HG12
|
B:VAL28
|
4.6
|
12.9
|
1.0
|
|
CG1
|
B:VAL28
|
4.6
|
13.0
|
1.0
|
|
HG12
|
B:ILE50
|
4.6
|
13.2
|
1.0
|
|
SG
|
B:CYS69
|
4.6
|
9.9
|
1.0
|
|
HG21
|
B:VAL28
|
4.7
|
12.7
|
1.0
|
|
N
|
B:GLY70
|
4.7
|
9.4
|
1.0
|
|
CG1
|
B:ILE50
|
4.7
|
13.2
|
1.0
|
|
SG
|
B:CYS66
|
4.7
|
10.3
|
1.0
|
|
HB
|
B:VAL28
|
4.8
|
12.2
|
1.0
|
|
HD11
|
B:ILE50
|
4.8
|
13.7
|
1.0
|
|
N
|
B:GLN71
|
4.8
|
10.0
|
1.0
|
|
SG
|
B:CYS45
|
4.8
|
10.5
|
1.0
|
|
CA
|
B:GLY70
|
4.8
|
9.5
|
1.0
|
|
HA
|
B:CYS45
|
4.9
|
10.4
|
1.0
|
|
HG12
|
B:ILE60
|
4.9
|
12.5
|
1.0
|
|
HG
|
B:CYS45
|
5.0
|
10.3
|
0.0
|
|
HA
|
B:CYS72
|
5.0
|
11.0
|
1.0
|
|
HG
|
B:CYS66
|
5.0
|
10.1
|
0.0
|
|
Iron binding site 3 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 3 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe505
b:9.7
occ:1.00
|
FE3
|
B:SF4505
|
0.0
|
9.7
|
1.0
|
|
S2
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
SG
|
B:CYS69
|
2.3
|
9.9
|
1.0
|
|
S4
|
B:SF4505
|
2.3
|
10.4
|
1.0
|
|
S1
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
FE2
|
B:SF4505
|
2.8
|
10.2
|
1.0
|
|
FE4
|
B:SF4505
|
2.8
|
9.8
|
1.0
|
|
FE1
|
B:SF4505
|
2.8
|
10.1
|
1.0
|
|
H
|
B:CYS69
|
2.9
|
8.9
|
1.0
|
|
HG
|
B:CYS69
|
3.1
|
9.7
|
0.0
|
|
H
|
B:GLY70
|
3.2
|
9.4
|
1.0
|
|
HD2
|
B:PRO46
|
3.5
|
11.1
|
1.0
|
|
H
|
B:GLN71
|
3.6
|
10.1
|
1.0
|
|
N
|
B:CYS69
|
3.6
|
9.1
|
1.0
|
|
CB
|
B:CYS69
|
3.6
|
9.7
|
1.0
|
|
N
|
B:GLY70
|
3.8
|
9.4
|
1.0
|
|
HB3
|
B:CYS69
|
3.8
|
9.6
|
1.0
|
|
S3
|
B:SF4505
|
3.9
|
10.3
|
1.0
|
|
CA
|
B:CYS69
|
4.0
|
8.9
|
1.0
|
|
H
|
B:ASN68
|
4.0
|
9.0
|
1.0
|
|
H
|
B:CYS72
|
4.0
|
10.8
|
1.0
|
|
HD3
|
B:PRO46
|
4.1
|
11.1
|
1.0
|
|
HG13
|
B:ILE67
|
4.1
|
9.9
|
1.0
|
|
HG12
|
B:ILE67
|
4.1
|
10.0
|
1.0
|
|
H
|
B:ILE67
|
4.2
|
8.9
|
1.0
|
|
CD
|
B:PRO46
|
4.2
|
11.2
|
1.0
|
|
C
|
B:CYS69
|
4.3
|
9.1
|
1.0
|
|
HA
|
B:CYS45
|
4.3
|
10.4
|
1.0
|
|
N
|
B:GLN71
|
4.3
|
10.0
|
1.0
|
|
HB2
|
B:GLN71
|
4.4
|
10.9
|
1.0
|
|
HB2
|
B:CYS69
|
4.4
|
9.6
|
1.0
|
|
N
|
B:ASN68
|
4.4
|
9.1
|
1.0
|
|
C
|
B:ASN68
|
4.6
|
9.3
|
1.0
|
|
CG1
|
B:ILE67
|
4.6
|
10.1
|
1.0
|
|
HA2
|
B:GLY70
|
4.6
|
9.5
|
1.0
|
|
SG
|
B:CYS72
|
4.6
|
10.9
|
1.0
|
|
CA
|
B:GLY70
|
4.7
|
9.5
|
1.0
|
|
HG3
|
B:PRO46
|
4.7
|
11.0
|
1.0
|
|
SG
|
B:CYS66
|
4.7
|
10.3
|
1.0
|
|
HA
|
B:ASN68
|
4.8
|
9.5
|
1.0
|
|
SG
|
B:CYS45
|
4.8
|
10.5
|
1.0
|
|
O
|
B:HOH760
|
4.8
|
11.7
|
1.0
|
|
CG
|
B:PRO46
|
4.9
|
11.0
|
1.0
|
|
CA
|
B:ASN68
|
4.9
|
9.6
|
1.0
|
|
HG
|
B:CYS72
|
4.9
|
10.5
|
0.0
|
|
N
|
B:ILE67
|
4.9
|
8.7
|
1.0
|
|
HG2
|
B:PRO46
|
4.9
|
11.2
|
1.0
|
|
HA
|
B:CYS69
|
4.9
|
9.0
|
1.0
|
|
N
|
B:CYS72
|
4.9
|
10.7
|
1.0
|
|
Iron binding site 4 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 4 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe505
b:9.8
occ:1.00
|
FE4
|
B:SF4505
|
0.0
|
9.8
|
1.0
|
|
S1
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
SG
|
B:CYS66
|
2.3
|
10.3
|
1.0
|
|
S3
|
B:SF4505
|
2.3
|
10.3
|
1.0
|
|
S2
|
B:SF4505
|
2.3
|
9.8
|
1.0
|
|
FE1
|
B:SF4505
|
2.7
|
10.1
|
1.0
|
|
FE2
|
B:SF4505
|
2.7
|
10.2
|
1.0
|
|
FE3
|
B:SF4505
|
2.8
|
9.7
|
1.0
|
|
HG
|
B:CYS66
|
3.0
|
10.1
|
0.0
|
|
H
|
B:ASN68
|
3.1
|
9.0
|
1.0
|
|
HA
|
B:CYS66
|
3.3
|
10.8
|
1.0
|
|
CB
|
B:CYS66
|
3.4
|
10.7
|
1.0
|
|
H
|
B:ILE67
|
3.4
|
8.9
|
1.0
|
|
HB2
|
B:CYS66
|
3.5
|
10.6
|
1.0
|
|
CA
|
B:CYS66
|
3.8
|
10.8
|
1.0
|
|
S4
|
B:SF4505
|
3.9
|
10.4
|
1.0
|
|
N
|
B:ASN68
|
3.9
|
9.1
|
1.0
|
|
N
|
B:ILE67
|
4.0
|
8.7
|
1.0
|
|
H
|
B:CYS69
|
4.0
|
8.9
|
1.0
|
|
HD13
|
B:ILE60
|
4.0
|
13.0
|
1.0
|
|
HB2
|
B:ALA49
|
4.0
|
11.6
|
1.0
|
|
HA
|
B:ASN68
|
4.1
|
9.5
|
1.0
|
|
HG21
|
B:ILE60
|
4.2
|
13.6
|
1.0
|
|
HB3
|
B:CYS66
|
4.2
|
10.7
|
1.0
|
|
C
|
B:CYS66
|
4.3
|
11.0
|
1.0
|
|
H
|
B:GLY70
|
4.5
|
9.4
|
1.0
|
|
HG
|
B:CYS72
|
4.5
|
10.5
|
0.0
|
|
HB
|
B:VAL28
|
4.6
|
12.2
|
1.0
|
|
CA
|
B:ASN68
|
4.6
|
9.6
|
1.0
|
|
N
|
B:CYS69
|
4.7
|
9.1
|
1.0
|
|
CB
|
B:ALA49
|
4.7
|
11.8
|
1.0
|
|
HB3
|
B:ALA49
|
4.7
|
11.6
|
1.0
|
|
SG
|
B:CYS45
|
4.8
|
10.5
|
1.0
|
|
HB1
|
B:ALA49
|
4.8
|
11.6
|
1.0
|
|
SG
|
B:CYS72
|
4.8
|
10.9
|
1.0
|
|
HG12
|
B:ILE67
|
4.9
|
10.0
|
1.0
|
|
CD1
|
B:ILE60
|
4.9
|
13.1
|
1.0
|
|
HG22
|
B:ILE60
|
4.9
|
13.6
|
1.0
|
|
C
|
B:ILE67
|
4.9
|
8.9
|
1.0
|
|
HG21
|
B:VAL28
|
4.9
|
12.7
|
1.0
|
|
HD2
|
B:PRO46
|
4.9
|
11.1
|
1.0
|
|
O
|
B:HOH722
|
4.9
|
19.0
|
1.0
|
|
HG13
|
B:VAL28
|
4.9
|
12.8
|
1.0
|
|
HD12
|
B:ILE60
|
5.0
|
13.0
|
1.0
|
|
HG
|
B:CYS45
|
5.0
|
10.3
|
0.0
|
|
SG
|
B:CYS69
|
5.0
|
9.9
|
1.0
|
|
Iron binding site 5 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 5 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe506
b:8.8
occ:1.00
|
FE1
|
B:SF4506
|
0.0
|
8.8
|
1.0
|
|
S4
|
B:SF4506
|
2.3
|
9.0
|
1.0
|
|
SG
|
B:CYS378
|
2.3
|
9.4
|
1.0
|
|
S3
|
B:SF4506
|
2.3
|
8.7
|
1.0
|
|
HG
|
B:CYS378
|
2.3
|
9.1
|
0.0
|
|
S2
|
B:SF4506
|
2.3
|
8.7
|
1.0
|
|
FE4
|
B:SF4506
|
2.7
|
8.5
|
1.0
|
|
FE3
|
B:SF4506
|
2.7
|
8.4
|
1.0
|
|
FE2
|
B:SF4506
|
2.8
|
8.6
|
1.0
|
|
HB2
|
B:CYS378
|
3.0
|
8.9
|
1.0
|
|
CB
|
B:CYS378
|
3.2
|
8.9
|
1.0
|
|
H
|
B:CYS378
|
3.3
|
9.2
|
1.0
|
|
HA2
|
B:GLY385
|
3.6
|
9.1
|
1.0
|
|
N
|
B:CYS378
|
3.8
|
9.3
|
1.0
|
|
HB2
|
B:ALA377
|
3.8
|
9.1
|
1.0
|
|
HA
|
B:CYS382
|
3.8
|
8.2
|
1.0
|
|
S1
|
B:SF4506
|
3.9
|
8.5
|
1.0
|
|
HB3
|
B:CYS378
|
4.0
|
9.0
|
1.0
|
|
HA3
|
B:GLY385
|
4.0
|
9.1
|
1.0
|
|
CA
|
B:CYS378
|
4.1
|
9.2
|
1.0
|
|
O
|
B:HOH684
|
4.2
|
9.8
|
1.0
|
|
H
|
B:GLY386
|
4.3
|
9.1
|
1.0
|
|
CA
|
B:GLY385
|
4.3
|
9.2
|
1.0
|
|
H
|
B:ALA377
|
4.3
|
8.8
|
1.0
|
|
SG
|
B:CYS234
|
4.5
|
8.6
|
1.0
|
|
HB2
|
B:CYS69
|
4.6
|
9.6
|
1.0
|
|
HA
|
B:CYS378
|
4.6
|
9.2
|
1.0
|
|
HG
|
B:CYS234
|
4.6
|
8.3
|
0.0
|
|
HA
|
B:CYS69
|
4.6
|
9.0
|
1.0
|
|
C
|
B:ALA377
|
4.6
|
8.8
|
1.0
|
|
CB
|
B:ALA377
|
4.7
|
9.0
|
1.0
|
|
N
|
B:ALA377
|
4.7
|
8.7
|
1.0
|
|
HB2
|
B:CYS234
|
4.7
|
8.2
|
1.0
|
|
SG
|
B:CYS179
|
4.7
|
8.4
|
1.0
|
|
HE21
|
B:GLN71
|
4.8
|
10.8
|
1.0
|
|
CA
|
B:CYS382
|
4.8
|
8.1
|
1.0
|
|
HG
|
B:CYS179
|
4.9
|
8.2
|
0.0
|
|
CA
|
B:ALA377
|
4.9
|
9.2
|
1.0
|
|
SG
|
B:CYS382
|
4.9
|
9.4
|
1.0
|
|
O
|
B:CYS69
|
4.9
|
9.6
|
1.0
|
|
Iron binding site 6 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 6 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe506
b:8.6
occ:1.00
|
FE2
|
B:SF4506
|
0.0
|
8.6
|
1.0
|
|
S3
|
B:SF4506
|
2.2
|
8.7
|
1.0
|
|
S1
|
B:SF4506
|
2.3
|
8.5
|
1.0
|
|
SG
|
B:CYS382
|
2.3
|
9.4
|
1.0
|
|
S4
|
B:SF4506
|
2.3
|
9.0
|
1.0
|
|
FE4
|
B:SF4506
|
2.7
|
8.5
|
1.0
|
|
FE3
|
B:SF4506
|
2.7
|
8.4
|
1.0
|
|
FE1
|
B:SF4506
|
2.8
|
8.8
|
1.0
|
|
HA
|
B:CYS382
|
2.8
|
8.2
|
1.0
|
|
HG
|
B:CYS382
|
3.2
|
9.0
|
0.0
|
|
CB
|
B:CYS382
|
3.3
|
8.1
|
1.0
|
|
H10
|
B:MHX508
|
3.3
|
9.6
|
0.9
|
|
CA
|
B:CYS382
|
3.4
|
8.1
|
1.0
|
|
HB3
|
B:CYS382
|
3.5
|
8.2
|
1.0
|
|
C3
|
B:MHX508
|
3.8
|
8.5
|
0.9
|
|
N
|
B:CYS382
|
3.9
|
8.4
|
1.0
|
|
S2
|
B:SF4506
|
3.9
|
8.7
|
1.0
|
|
O3
|
B:MHX508
|
4.0
|
9.7
|
0.9
|
|
FE1
|
B:MHX508
|
4.1
|
9.8
|
0.9
|
|
H
|
B:CYS382
|
4.1
|
8.5
|
1.0
|
|
HB2
|
B:CYS382
|
4.2
|
8.2
|
1.0
|
|
HB2
|
B:CYS234
|
4.2
|
8.2
|
1.0
|
|
HG
|
B:CYS234
|
4.2
|
8.3
|
0.0
|
|
C2
|
B:MHX508
|
4.3
|
9.4
|
0.9
|
|
HG2
|
B:PRO233
|
4.4
|
8.1
|
1.0
|
|
S2
|
B:MHX508
|
4.4
|
9.5
|
0.9
|
|
HB2
|
B:CYS378
|
4.6
|
8.9
|
1.0
|
|
HS2
|
B:MHX508
|
4.6
|
9.5
|
0.9
|
|
C
|
B:GLY381
|
4.6
|
9.2
|
1.0
|
|
HG
|
B:CYS378
|
4.6
|
9.1
|
0.0
|
|
H11
|
B:MHX508
|
4.7
|
9.8
|
0.9
|
|
HB2
|
B:CYS179
|
4.7
|
8.4
|
1.0
|
|
SD
|
B:MET376
|
4.7
|
9.8
|
1.0
|
|
SG
|
B:CYS234
|
4.7
|
8.6
|
1.0
|
|
C
|
B:CYS382
|
4.8
|
8.5
|
1.0
|
|
HA3
|
B:GLY385
|
4.8
|
9.1
|
1.0
|
|
HB3
|
B:MET376
|
4.8
|
9.3
|
1.0
|
|
SG
|
B:CYS179
|
4.8
|
8.4
|
1.0
|
|
HA
|
B:CYS179
|
4.8
|
8.1
|
1.0
|
|
H9
|
B:MHX508
|
4.8
|
9.8
|
0.9
|
|
H
|
B:CYS378
|
4.8
|
9.2
|
1.0
|
|
HD2
|
B:PRO180
|
4.9
|
8.2
|
1.0
|
|
SG
|
B:CYS378
|
4.9
|
9.4
|
1.0
|
|
CB
|
B:CYS234
|
4.9
|
8.1
|
1.0
|
|
HA2
|
B:GLY381
|
5.0
|
9.4
|
1.0
|
|
O
|
B:CYS382
|
5.0
|
8.7
|
1.0
|
|
Iron binding site 7 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 7 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe506
b:8.4
occ:1.00
|
FE3
|
B:SF4506
|
0.0
|
8.4
|
1.0
|
|
S2
|
B:SF4506
|
2.2
|
8.7
|
1.0
|
|
SG
|
B:CYS179
|
2.3
|
8.4
|
1.0
|
|
S1
|
B:SF4506
|
2.3
|
8.5
|
1.0
|
|
S4
|
B:SF4506
|
2.3
|
9.0
|
1.0
|
|
FE4
|
B:SF4506
|
2.7
|
8.5
|
1.0
|
|
FE1
|
B:SF4506
|
2.7
|
8.8
|
1.0
|
|
FE2
|
B:SF4506
|
2.7
|
8.6
|
1.0
|
|
HG
|
B:CYS179
|
2.8
|
8.2
|
0.0
|
|
H
|
B:ALA377
|
3.1
|
8.8
|
1.0
|
|
HB2
|
B:CYS179
|
3.3
|
8.4
|
1.0
|
|
CB
|
B:CYS179
|
3.4
|
8.6
|
1.0
|
|
HB2
|
B:ALA377
|
3.4
|
9.1
|
1.0
|
|
HA
|
B:CYS179
|
3.5
|
8.1
|
1.0
|
|
H
|
B:GLY181
|
3.6
|
8.1
|
1.0
|
|
HD2
|
B:PRO180
|
3.7
|
8.2
|
1.0
|
|
S3
|
B:SF4506
|
3.9
|
8.7
|
1.0
|
|
CA
|
B:CYS179
|
3.9
|
8.0
|
1.0
|
|
N
|
B:ALA377
|
4.0
|
8.7
|
1.0
|
|
H10
|
B:MHX508
|
4.0
|
9.6
|
0.9
|
|
H
|
B:CYS378
|
4.0
|
9.2
|
1.0
|
|
HA
|
B:MET376
|
4.2
|
9.0
|
1.0
|
|
HB3
|
B:CYS179
|
4.2
|
8.4
|
1.0
|
|
CB
|
B:ALA377
|
4.2
|
9.0
|
1.0
|
|
HG
|
B:CYS234
|
4.3
|
8.3
|
0.0
|
|
HB1
|
B:ALA377
|
4.3
|
9.0
|
1.0
|
|
HA3
|
B:GLY181
|
4.3
|
8.3
|
1.0
|
|
C
|
B:CYS179
|
4.4
|
8.0
|
1.0
|
|
H
|
B:TRP182
|
4.4
|
8.1
|
1.0
|
|
N
|
B:GLY181
|
4.4
|
8.3
|
1.0
|
|
N
|
B:PRO180
|
4.5
|
7.8
|
1.0
|
|
CD
|
B:PRO180
|
4.5
|
8.2
|
1.0
|
|
CA
|
B:ALA377
|
4.6
|
9.2
|
1.0
|
|
HB3
|
B:MET376
|
4.7
|
9.3
|
1.0
|
|
HG2
|
B:PRO180
|
4.7
|
8.5
|
1.0
|
|
SG
|
B:CYS378
|
4.7
|
9.4
|
1.0
|
|
SG
|
B:CYS382
|
4.7
|
9.4
|
1.0
|
|
N
|
B:CYS378
|
4.8
|
9.3
|
1.0
|
|
SG
|
B:CYS234
|
4.8
|
8.6
|
1.0
|
|
H9
|
B:MHX508
|
4.8
|
9.8
|
0.9
|
|
C2
|
B:MHX508
|
4.9
|
9.4
|
0.9
|
|
C
|
B:MET376
|
4.9
|
9.1
|
1.0
|
|
SD
|
B:MET376
|
4.9
|
9.8
|
1.0
|
|
CA
|
B:MET376
|
4.9
|
8.8
|
1.0
|
|
CA
|
B:GLY181
|
4.9
|
8.3
|
1.0
|
|
HB2
|
B:ALA236
|
5.0
|
8.8
|
1.0
|
|
Iron binding site 8 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 8 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe506
b:8.5
occ:1.00
|
FE4
|
B:SF4506
|
0.0
|
8.5
|
1.0
|
|
HG
|
B:CYS234
|
2.0
|
8.3
|
0.0
|
|
S1
|
B:SF4506
|
2.3
|
8.5
|
1.0
|
|
SG
|
B:CYS234
|
2.3
|
8.6
|
1.0
|
|
S2
|
B:SF4506
|
2.3
|
8.7
|
1.0
|
|
S3
|
B:SF4506
|
2.3
|
8.7
|
1.0
|
|
FE3
|
B:SF4506
|
2.7
|
8.4
|
1.0
|
|
FE1
|
B:SF4506
|
2.7
|
8.8
|
1.0
|
|
FE2
|
B:SF4506
|
2.7
|
8.6
|
1.0
|
|
HB2
|
B:CYS234
|
3.0
|
8.2
|
1.0
|
|
CB
|
B:CYS234
|
3.2
|
8.1
|
1.0
|
|
HB2
|
B:ALA236
|
3.7
|
8.8
|
1.0
|
|
HD2
|
B:PRO180
|
3.8
|
8.2
|
1.0
|
|
S4
|
B:SF4506
|
3.8
|
9.0
|
1.0
|
|
HB3
|
B:CYS234
|
3.9
|
8.2
|
1.0
|
|
O
|
B:HOH684
|
3.9
|
9.8
|
1.0
|
|
HG2
|
B:LYS237
|
4.0
|
7.9
|
1.0
|
|
O3
|
B:MHX508
|
4.0
|
9.7
|
0.9
|
|
HG2
|
B:PRO180
|
4.0
|
8.5
|
1.0
|
|
HA
|
B:CYS234
|
4.1
|
8.3
|
1.0
|
|
HE2
|
B:LYS237
|
4.2
|
7.9
|
1.0
|
|
CA
|
B:CYS234
|
4.3
|
8.4
|
1.0
|
|
HG
|
B:CYS378
|
4.4
|
9.1
|
0.0
|
|
H
|
B:GLY181
|
4.4
|
8.1
|
1.0
|
|
C3
|
B:MHX508
|
4.5
|
8.5
|
0.9
|
|
H
|
B:LYS237
|
4.5
|
7.7
|
1.0
|
|
H
|
B:ALA236
|
4.6
|
8.4
|
1.0
|
|
CD
|
B:PRO180
|
4.6
|
8.2
|
1.0
|
|
CB
|
B:ALA236
|
4.6
|
8.8
|
1.0
|
|
SG
|
B:CYS378
|
4.7
|
9.4
|
1.0
|
|
CG
|
B:PRO180
|
4.7
|
8.7
|
1.0
|
|
SG
|
B:CYS382
|
4.7
|
9.4
|
1.0
|
|
SG
|
B:CYS179
|
4.7
|
8.4
|
1.0
|
|
HG2
|
B:PRO233
|
4.7
|
8.1
|
1.0
|
|
HA
|
B:CYS382
|
4.8
|
8.2
|
1.0
|
|
HB1
|
B:ALA236
|
4.8
|
8.8
|
1.0
|
|
HA
|
B:CYS179
|
4.8
|
8.1
|
1.0
|
|
CG
|
B:LYS237
|
4.8
|
7.8
|
1.0
|
|
HA3
|
B:GLY385
|
4.9
|
9.1
|
1.0
|
|
HG3
|
B:LYS237
|
4.9
|
7.9
|
1.0
|
|
H
|
B:GLY386
|
4.9
|
9.1
|
1.0
|
|
HS2
|
B:MHX508
|
4.9
|
9.5
|
0.9
|
|
HG3
|
B:PRO180
|
5.0
|
8.6
|
1.0
|
|
HA
|
B:CYS69
|
5.0
|
9.0
|
1.0
|
|
Iron binding site 9 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 9 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe507
b:13.8
occ:1.00
|
FE1
|
B:SF4507
|
0.0
|
13.8
|
1.0
|
|
HG
|
B:CYS41
|
2.2
|
12.8
|
0.0
|
|
S4
|
B:SF4507
|
2.3
|
14.8
|
1.0
|
|
SG
|
B:CYS41
|
2.3
|
13.0
|
1.0
|
|
S2
|
B:SF4507
|
2.3
|
13.8
|
1.0
|
|
S3
|
B:SF4507
|
2.3
|
15.3
|
1.0
|
|
FE4
|
B:SF4507
|
2.7
|
15.1
|
1.0
|
|
FE2
|
B:SF4507
|
2.7
|
15.7
|
1.0
|
|
FE3
|
B:SF4507
|
2.7
|
14.2
|
1.0
|
|
HB3
|
B:CYS41
|
2.9
|
12.9
|
1.0
|
|
H
|
B:CYS41
|
3.1
|
12.8
|
1.0
|
|
CB
|
B:CYS41
|
3.2
|
13.2
|
1.0
|
|
HD12
|
B:ILE81
|
3.5
|
12.9
|
1.0
|
|
N
|
B:CYS41
|
3.9
|
12.9
|
1.0
|
|
S1
|
B:SF4507
|
3.9
|
16.1
|
1.0
|
|
HB2
|
B:CYS41
|
3.9
|
13.1
|
1.0
|
|
HB2
|
B:HIS58
|
3.9
|
13.2
|
1.0
|
|
HD13
|
B:ILE30
|
4.1
|
12.9
|
1.0
|
|
H
|
B:ASP39
|
4.2
|
16.0
|
1.0
|
|
HD2
|
B:HIS58
|
4.2
|
13.0
|
1.0
|
|
CA
|
B:CYS41
|
4.2
|
12.4
|
1.0
|
|
H
|
B:THR40
|
4.4
|
14.2
|
1.0
|
|
CD2
|
B:HIS58
|
4.4
|
12.9
|
1.0
|
|
H
|
B:SER42
|
4.4
|
11.9
|
1.0
|
|
CD1
|
B:ILE81
|
4.5
|
13.1
|
1.0
|
|
CG
|
B:HIS58
|
4.6
|
12.8
|
1.0
|
|
SG
|
B:CYS35
|
4.6
|
15.7
|
1.0
|
|
CB
|
B:HIS58
|
4.6
|
13.3
|
1.0
|
|
HB2
|
B:CYS76
|
4.6
|
13.7
|
1.0
|
|
HB3
|
B:HIS58
|
4.6
|
13.2
|
1.0
|
|
HB
|
B:THR40
|
4.6
|
15.5
|
1.0
|
|
SG
|
B:CYS38
|
4.7
|
18.1
|
1.0
|
|
HG21
|
B:ILE50
|
4.7
|
12.9
|
1.0
|
|
N
|
B:THR40
|
4.7
|
14.1
|
1.0
|
|
HG
|
B:CYS35
|
4.8
|
15.4
|
0.0
|
|
HA
|
B:ASP39
|
4.8
|
15.5
|
1.0
|
|
SG
|
B:CYS76
|
4.8
|
14.3
|
1.0
|
|
HG13
|
B:ILE81
|
4.8
|
12.5
|
1.0
|
|
N
|
B:ASP39
|
4.8
|
16.1
|
1.0
|
|
HA
|
B:CYS41
|
4.8
|
12.6
|
1.0
|
|
H
|
B:CYS38
|
4.8
|
17.3
|
1.0
|
|
HD13
|
B:ILE81
|
4.9
|
13.0
|
1.0
|
|
HA
|
B:CYS76
|
4.9
|
13.8
|
1.0
|
|
HD11
|
B:ILE81
|
4.9
|
12.9
|
1.0
|
|
HG
|
B:CYS76
|
4.9
|
13.7
|
0.0
|
|
HD2
|
B:PRO77
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 10 out
of 14 in 8ru6
Go back to
Iron Binding Sites List in 8ru6
Iron binding site 10 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A 4 Amino Acid Linker Peptide Derived From Cpi of Clostridium Pasteurianum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe507
b:15.7
occ:1.00
|
FE2
|
B:SF4507
|
0.0
|
15.7
|
1.0
|
|
S3
|
B:SF4507
|
2.3
|
15.3
|
1.0
|
|
S1
|
B:SF4507
|
2.3
|
16.1
|
1.0
|
|
SG
|
B:CYS38
|
2.3
|
18.1
|
1.0
|
|
S4
|
B:SF4507
|
2.3
|
14.8
|
1.0
|
|
FE1
|
B:SF4507
|
2.7
|
13.8
|
1.0
|
|
FE3
|
B:SF4507
|
2.7
|
14.2
|
1.0
|
|
FE4
|
B:SF4507
|
2.7
|
15.1
|
1.0
|
|
H
|
B:CYS38
|
2.8
|
17.3
|
1.0
|
|
HG
|
B:CYS38
|
3.1
|
17.4
|
0.0
|
|
H
|
B:ASP39
|
3.3
|
16.0
|
1.0
|
|
H
|
B:THR40
|
3.5
|
14.2
|
1.0
|
|
N
|
B:CYS38
|
3.5
|
17.2
|
1.0
|
|
HD2
|
B:PRO77
|
3.5
|
16.8
|
1.0
|
|
CB
|
B:CYS38
|
3.6
|
18.1
|
1.0
|
|
HB3
|
B:CYS38
|
3.8
|
17.9
|
1.0
|
|
H
|
B:GLY37
|
3.9
|
18.6
|
1.0
|
|
S2
|
B:SF4507
|
3.9
|
13.8
|
1.0
|
|
N
|
B:ASP39
|
3.9
|
16.1
|
1.0
|
|
CA
|
B:CYS38
|
3.9
|
17.4
|
1.0
|
|
H
|
B:CYS41
|
4.0
|
12.8
|
1.0
|
|
HB
|
B:THR40
|
4.0
|
15.5
|
1.0
|
|
HG12
|
B:ILE36
|
4.2
|
21.3
|
1.0
|
|
HG13
|
B:ILE36
|
4.2
|
21.4
|
1.0
|
|
C
|
B:CYS38
|
4.3
|
16.3
|
1.0
|
|
N
|
B:THR40
|
4.3
|
14.1
|
1.0
|
|
H
|
B:ILE36
|
4.3
|
17.5
|
1.0
|
|
N
|
B:GLY37
|
4.4
|
18.8
|
1.0
|
|
HB2
|
B:CYS38
|
4.4
|
18.0
|
1.0
|
|
CD
|
B:PRO77
|
4.5
|
16.8
|
1.0
|
|
HG2
|
B:PRO77
|
4.5
|
19.2
|
1.0
|
|
C
|
B:GLY37
|
4.5
|
17.4
|
1.0
|
|
HA2
|
B:GLY37
|
4.6
|
18.4
|
1.0
|
|
SG
|
B:CYS41
|
4.6
|
13.0
|
1.0
|
|
SG
|
B:CYS76
|
4.7
|
14.3
|
1.0
|
|
HA
|
B:CYS76
|
4.7
|
13.8
|
1.0
|
|
SG
|
B:CYS35
|
4.7
|
15.7
|
1.0
|
|
CG1
|
B:ILE36
|
4.7
|
21.5
|
1.0
|
|
CA
|
B:GLY37
|
4.8
|
18.6
|
1.0
|
|
CB
|
B:THR40
|
4.8
|
15.2
|
1.0
|
|
HD3
|
B:PRO77
|
4.8
|
16.8
|
1.0
|
|
HG2
|
B:GLU78
|
4.8
|
19.9
|
1.0
|
|
HG
|
B:CYS41
|
4.8
|
12.8
|
0.0
|
|
HA
|
B:CYS38
|
4.9
|
17.3
|
1.0
|
|
CG
|
B:PRO77
|
4.9
|
20.1
|
1.0
|
|
OG1
|
B:THR40
|
4.9
|
16.7
|
1.0
|
|
N
|
B:CYS41
|
4.9
|
12.9
|
1.0
|
|
CA
|
B:ASP39
|
4.9
|
15.5
|
1.0
|
|
HA
|
B:ASP39
|
5.0
|
15.5
|
1.0
|
|
N
|
B:ILE36
|
5.0
|
17.3
|
1.0
|
|
HB3
|
B:CYS41
|
5.0
|
12.9
|
1.0
|
|
Reference:
K.Bikbaev,
J.Jaenecke,
M.Winkler,
I.Span.
Enhancing Maturation of [Fefe]-Hydrogenase By Interlinking the Large and Small Subunits To Be Published.
Page generated: Tue Feb 25 09:44:19 2025
|
