Iron in PDB 8ryh: Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
Enzymatic activity of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica:
1.12.7.2;
Protein crystallography data
The structure of Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica, PDB code: 8ryh
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)
|
45.40 /
1.77
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.118,
50.603,
86.643,
90,
105.33,
90
|
R / Rfree (%)
|
20.5 /
24.6
|
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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
(pdb code 8ryh). 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica, PDB code: 8ryh:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 1 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:14.9
occ:1.00
|
FE1
|
A:SF4501
|
0.0
|
14.9
|
1.0
|
HG
|
A:CYS72
|
2.1
|
12.9
|
0.0
|
S3
|
A:SF4501
|
2.2
|
17.4
|
1.0
|
SG
|
A:CYS72
|
2.3
|
12.9
|
1.0
|
S2
|
A:SF4501
|
2.3
|
15.1
|
1.0
|
S4
|
A:SF4501
|
2.3
|
16.1
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
16.1
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
14.8
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
14.7
|
1.0
|
HB3
|
A:CYS72
|
3.0
|
14.3
|
1.0
|
H
|
A:CYS72
|
3.2
|
15.4
|
1.0
|
CB
|
A:CYS72
|
3.3
|
14.4
|
1.0
|
HD12
|
A:ILE50
|
3.4
|
22.1
|
1.0
|
HG13
|
A:VAL28
|
3.8
|
22.3
|
1.0
|
S1
|
A:SF4501
|
3.9
|
17.4
|
1.0
|
HB2
|
A:CYS72
|
3.9
|
14.2
|
1.0
|
H
|
A:GLY70
|
4.0
|
12.6
|
1.0
|
N
|
A:CYS72
|
4.0
|
15.7
|
1.0
|
HD12
|
A:ILE60
|
4.2
|
21.5
|
1.0
|
H
|
A:GLN71
|
4.3
|
14.9
|
1.0
|
CA
|
A:CYS72
|
4.3
|
14.9
|
1.0
|
CD1
|
A:ILE50
|
4.3
|
22.7
|
1.0
|
HG13
|
A:ILE50
|
4.3
|
21.1
|
1.0
|
HD13
|
A:ILE60
|
4.3
|
21.5
|
1.0
|
HA2
|
A:GLY70
|
4.4
|
12.9
|
1.0
|
HG12
|
A:VAL28
|
4.4
|
22.4
|
1.0
|
H
|
A:LEU73
|
4.4
|
14.2
|
1.0
|
HB2
|
A:CYS45
|
4.4
|
17.4
|
1.0
|
CG1
|
A:VAL28
|
4.6
|
22.8
|
1.0
|
HD11
|
A:ILE50
|
4.6
|
22.2
|
1.0
|
N
|
A:GLY70
|
4.6
|
12.0
|
1.0
|
N
|
A:GLN71
|
4.7
|
14.6
|
1.0
|
SG
|
A:CYS66
|
4.7
|
18.5
|
1.0
|
HG12
|
A:ILE50
|
4.7
|
21.2
|
1.0
|
CG1
|
A:ILE50
|
4.7
|
21.4
|
1.0
|
SG
|
A:CYS69
|
4.7
|
14.3
|
1.0
|
SG
|
A:CYS45
|
4.7
|
17.9
|
1.0
|
CD1
|
A:ILE60
|
4.7
|
21.9
|
1.0
|
CA
|
A:GLY70
|
4.8
|
12.8
|
1.0
|
HG12
|
A:ILE60
|
4.8
|
20.6
|
1.0
|
HA
|
A:CYS45
|
4.8
|
18.2
|
1.0
|
HG
|
A:CYS45
|
4.9
|
17.9
|
0.0
|
HA
|
A:CYS72
|
4.9
|
14.8
|
1.0
|
HD13
|
A:ILE50
|
4.9
|
22.2
|
1.0
|
HG
|
A:CYS66
|
4.9
|
18.5
|
0.0
|
HD2
|
A:PRO46
|
4.9
|
16.0
|
1.0
|
HB
|
A:VAL28
|
5.0
|
21.3
|
1.0
|
HB2
|
A:ALA49
|
5.0
|
17.9
|
1.0
|
C
|
A:GLY70
|
5.0
|
14.0
|
1.0
|
H
|
A:CYS69
|
5.0
|
13.3
|
1.0
|
|
Iron binding site 2 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 2 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:16.1
occ:1.00
|
FE2
|
A:SF4501
|
0.0
|
16.1
|
1.0
|
S4
|
A:SF4501
|
2.2
|
16.1
|
1.0
|
SG
|
A:CYS45
|
2.3
|
17.9
|
1.0
|
S3
|
A:SF4501
|
2.3
|
17.4
|
1.0
|
S1
|
A:SF4501
|
2.3
|
17.4
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
14.8
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
14.9
|
1.0
|
HG
|
A:CYS45
|
2.7
|
17.9
|
0.0
|
FE4
|
A:SF4501
|
2.8
|
14.7
|
1.0
|
HD2
|
A:PRO46
|
2.8
|
16.0
|
1.0
|
HB2
|
A:CYS45
|
3.1
|
17.4
|
1.0
|
HB2
|
A:ALA49
|
3.1
|
17.9
|
1.0
|
CB
|
A:CYS45
|
3.2
|
17.0
|
1.0
|
HA
|
A:CYS45
|
3.3
|
18.2
|
1.0
|
HG1
|
A:THR47
|
3.7
|
17.6
|
0.0
|
HG13
|
A:ILE50
|
3.7
|
21.1
|
1.0
|
CA
|
A:CYS45
|
3.8
|
18.0
|
1.0
|
CD
|
A:PRO46
|
3.8
|
16.0
|
1.0
|
S2
|
A:SF4501
|
3.9
|
15.1
|
1.0
|
HD12
|
A:ILE50
|
3.9
|
22.1
|
1.0
|
CB
|
A:ALA49
|
4.0
|
18.0
|
1.0
|
HB3
|
A:CYS45
|
4.1
|
17.4
|
1.0
|
H
|
A:ALA49
|
4.1
|
18.8
|
1.0
|
HD3
|
A:PRO46
|
4.2
|
16.0
|
1.0
|
OG1
|
A:THR47
|
4.2
|
17.6
|
1.0
|
HB1
|
A:ALA49
|
4.2
|
17.9
|
1.0
|
HD11
|
A:ILE50
|
4.3
|
22.2
|
1.0
|
H
|
A:THR47
|
4.3
|
18.6
|
1.0
|
HG
|
A:CYS72
|
4.3
|
12.9
|
0.0
|
HB3
|
A:CYS72
|
4.4
|
14.3
|
1.0
|
HA
|
A:CYS66
|
4.4
|
17.2
|
1.0
|
CD1
|
A:ILE50
|
4.4
|
22.7
|
1.0
|
CG1
|
A:ILE50
|
4.5
|
21.4
|
1.0
|
HG2
|
A:PRO46
|
4.5
|
16.0
|
1.0
|
HB3
|
A:ALA49
|
4.5
|
17.9
|
1.0
|
N
|
A:PRO46
|
4.5
|
16.0
|
1.0
|
C
|
A:CYS45
|
4.6
|
17.9
|
1.0
|
H
|
A:ILE67
|
4.6
|
14.9
|
1.0
|
CG
|
A:PRO46
|
4.7
|
15.9
|
1.0
|
SG
|
A:CYS72
|
4.8
|
12.9
|
1.0
|
N
|
A:ALA49
|
4.8
|
18.8
|
1.0
|
SG
|
A:CYS66
|
4.8
|
18.5
|
1.0
|
SG
|
A:CYS69
|
4.8
|
14.3
|
1.0
|
HG12
|
A:ILE50
|
4.9
|
21.2
|
1.0
|
H
|
A:ILE50
|
4.9
|
17.6
|
1.0
|
N
|
A:CYS45
|
5.0
|
20.3
|
1.0
|
CA
|
A:ALA49
|
5.0
|
17.8
|
1.0
|
H
|
A:CYS72
|
5.0
|
15.4
|
1.0
|
|
Iron binding site 3 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 3 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:14.8
occ:1.00
|
FE3
|
A:SF4501
|
0.0
|
14.8
|
1.0
|
SG
|
A:CYS66
|
2.3
|
18.5
|
1.0
|
S4
|
A:SF4501
|
2.3
|
16.1
|
1.0
|
S2
|
A:SF4501
|
2.3
|
15.1
|
1.0
|
S1
|
A:SF4501
|
2.3
|
17.4
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
16.1
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
14.9
|
1.0
|
FE4
|
A:SF4501
|
2.8
|
14.7
|
1.0
|
HG
|
A:CYS66
|
3.0
|
18.5
|
0.0
|
H
|
A:ASN68
|
3.2
|
13.4
|
1.0
|
HA
|
A:CYS66
|
3.3
|
17.2
|
1.0
|
H
|
A:ILE67
|
3.3
|
14.9
|
1.0
|
CB
|
A:CYS66
|
3.4
|
17.1
|
1.0
|
HB2
|
A:CYS66
|
3.5
|
17.5
|
1.0
|
CA
|
A:CYS66
|
3.7
|
17.6
|
1.0
|
HB2
|
A:ALA49
|
3.8
|
17.9
|
1.0
|
S3
|
A:SF4501
|
3.8
|
17.4
|
1.0
|
N
|
A:ILE67
|
3.9
|
14.4
|
1.0
|
N
|
A:ASN68
|
4.0
|
13.4
|
1.0
|
H
|
A:CYS69
|
4.0
|
13.3
|
1.0
|
HA
|
A:ASN68
|
4.1
|
13.6
|
1.0
|
C
|
A:CYS66
|
4.2
|
16.6
|
1.0
|
HB3
|
A:CYS66
|
4.2
|
17.5
|
1.0
|
HD13
|
A:ILE60
|
4.3
|
21.5
|
1.0
|
HG
|
A:CYS72
|
4.4
|
12.9
|
0.0
|
HG21
|
A:ILE60
|
4.4
|
20.5
|
1.0
|
HB3
|
A:ALA49
|
4.4
|
17.9
|
1.0
|
H
|
A:GLY70
|
4.4
|
12.6
|
1.0
|
CB
|
A:ALA49
|
4.4
|
18.0
|
1.0
|
HB1
|
A:ALA49
|
4.6
|
17.9
|
1.0
|
CA
|
A:ASN68
|
4.6
|
13.6
|
1.0
|
N
|
A:CYS69
|
4.7
|
13.4
|
1.0
|
SG
|
A:CYS45
|
4.7
|
17.9
|
1.0
|
HG12
|
A:ILE67
|
4.8
|
15.1
|
1.0
|
SG
|
A:CYS72
|
4.8
|
12.9
|
1.0
|
HD2
|
A:PRO46
|
4.8
|
16.0
|
1.0
|
HG22
|
A:ILE60
|
4.9
|
20.5
|
1.0
|
HG
|
A:CYS45
|
4.9
|
17.9
|
0.0
|
C
|
A:ILE67
|
4.9
|
13.1
|
1.0
|
HB
|
A:VAL28
|
4.9
|
21.3
|
1.0
|
HG12
|
A:ILE60
|
4.9
|
20.6
|
1.0
|
HG1
|
A:THR47
|
4.9
|
17.6
|
0.0
|
|
Iron binding site 4 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 4 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:14.7
occ:1.00
|
FE4
|
A:SF4501
|
0.0
|
14.7
|
1.0
|
S3
|
A:SF4501
|
2.2
|
17.4
|
1.0
|
S1
|
A:SF4501
|
2.3
|
17.4
|
1.0
|
S2
|
A:SF4501
|
2.3
|
15.1
|
1.0
|
SG
|
A:CYS69
|
2.4
|
14.3
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
14.9
|
1.0
|
FE3
|
A:SF4501
|
2.8
|
14.8
|
1.0
|
FE2
|
A:SF4501
|
2.8
|
16.1
|
1.0
|
H
|
A:CYS69
|
2.9
|
13.3
|
1.0
|
H
|
A:GLY70
|
3.1
|
12.6
|
1.0
|
HG
|
A:CYS69
|
3.2
|
14.3
|
0.0
|
H
|
A:GLN71
|
3.4
|
14.9
|
1.0
|
HD2
|
A:PRO46
|
3.4
|
16.0
|
1.0
|
N
|
A:CYS69
|
3.6
|
13.4
|
1.0
|
CB
|
A:CYS69
|
3.7
|
13.2
|
1.0
|
N
|
A:GLY70
|
3.8
|
12.0
|
1.0
|
S4
|
A:SF4501
|
3.9
|
16.1
|
1.0
|
HB3
|
A:CYS69
|
3.9
|
13.3
|
1.0
|
HD3
|
A:PRO46
|
4.0
|
16.0
|
1.0
|
HG12
|
A:ILE67
|
4.0
|
15.1
|
1.0
|
H
|
A:CYS72
|
4.0
|
15.4
|
1.0
|
CA
|
A:CYS69
|
4.0
|
13.1
|
1.0
|
CD
|
A:PRO46
|
4.1
|
16.0
|
1.0
|
H
|
A:ILE67
|
4.1
|
14.9
|
1.0
|
H
|
A:ASN68
|
4.1
|
13.4
|
1.0
|
N
|
A:GLN71
|
4.2
|
14.6
|
1.0
|
HA
|
A:CYS45
|
4.3
|
18.2
|
1.0
|
HB2
|
A:GLN71
|
4.3
|
18.9
|
1.0
|
HG13
|
A:ILE67
|
4.3
|
15.1
|
1.0
|
C
|
A:CYS69
|
4.3
|
13.8
|
1.0
|
HG3
|
A:PRO46
|
4.4
|
16.0
|
1.0
|
HB2
|
A:CYS69
|
4.5
|
13.3
|
1.0
|
N
|
A:ASN68
|
4.5
|
13.4
|
1.0
|
C
|
A:ASN68
|
4.6
|
13.4
|
1.0
|
CG1
|
A:ILE67
|
4.6
|
14.5
|
1.0
|
SG
|
A:CYS72
|
4.6
|
12.9
|
1.0
|
CG
|
A:PRO46
|
4.7
|
15.9
|
1.0
|
SG
|
A:CYS66
|
4.7
|
18.5
|
1.0
|
HG2
|
A:PRO46
|
4.7
|
16.0
|
1.0
|
CA
|
A:GLY70
|
4.7
|
12.8
|
1.0
|
HA2
|
A:GLY70
|
4.7
|
12.9
|
1.0
|
SG
|
A:CYS45
|
4.8
|
17.9
|
1.0
|
HA
|
A:ASN68
|
4.8
|
13.6
|
1.0
|
HG
|
A:CYS72
|
4.8
|
12.9
|
0.0
|
N
|
A:ILE67
|
4.9
|
14.4
|
1.0
|
CA
|
A:ASN68
|
4.9
|
13.6
|
1.0
|
N
|
A:CYS72
|
4.9
|
15.7
|
1.0
|
C
|
A:GLY70
|
4.9
|
14.0
|
1.0
|
O
|
A:HOH684
|
5.0
|
10.7
|
1.0
|
HB3
|
A:CYS72
|
5.0
|
14.3
|
1.0
|
HA
|
A:CYS69
|
5.0
|
13.3
|
1.0
|
|
Iron binding site 5 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 5 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:17.8
occ:1.00
|
FE1
|
A:SF4502
|
0.0
|
17.8
|
1.0
|
S3
|
A:SF4502
|
2.3
|
18.1
|
1.0
|
SG
|
A:CYS35
|
2.3
|
21.3
|
1.0
|
S2
|
A:SF4502
|
2.3
|
17.3
|
1.0
|
S4
|
A:SF4502
|
2.3
|
18.7
|
1.0
|
FE4
|
A:SF4502
|
2.7
|
16.3
|
1.0
|
FE3
|
A:SF4502
|
2.7
|
18.6
|
1.0
|
FE2
|
A:SF4502
|
2.7
|
20.2
|
1.0
|
HG
|
A:CYS35
|
3.0
|
21.3
|
0.0
|
HA
|
A:CYS35
|
3.1
|
19.7
|
1.0
|
H
|
A:GLY37
|
3.2
|
23.4
|
1.0
|
CB
|
A:CYS35
|
3.3
|
19.9
|
1.0
|
HB2
|
A:CYS35
|
3.4
|
20.0
|
1.0
|
HB2
|
A:HIS58
|
3.5
|
21.4
|
1.0
|
H
|
A:ILE36
|
3.5
|
23.4
|
1.0
|
CA
|
A:CYS35
|
3.6
|
19.2
|
1.0
|
S1
|
A:SF4502
|
3.8
|
19.7
|
1.0
|
H
|
A:CYS38
|
4.0
|
24.0
|
1.0
|
N
|
A:GLY37
|
4.0
|
23.0
|
1.0
|
HB2
|
A:ALA80
|
4.0
|
15.9
|
1.0
|
N
|
A:ILE36
|
4.0
|
23.6
|
1.0
|
HA2
|
A:GLY37
|
4.1
|
24.0
|
1.0
|
H
|
A:HIS58
|
4.1
|
22.1
|
1.0
|
HG21
|
A:ILE30
|
4.2
|
18.2
|
1.0
|
HB3
|
A:CYS35
|
4.2
|
20.0
|
1.0
|
C
|
A:CYS35
|
4.2
|
21.9
|
1.0
|
HG
|
A:CYS41
|
4.3
|
20.2
|
0.0
|
HG22
|
A:ILE30
|
4.4
|
18.2
|
1.0
|
CB
|
A:HIS58
|
4.4
|
20.9
|
1.0
|
H
|
A:ASP39
|
4.5
|
23.0
|
1.0
|
HB3
|
A:ALA80
|
4.5
|
15.9
|
1.0
|
CA
|
A:GLY37
|
4.5
|
24.2
|
1.0
|
CB
|
A:ALA80
|
4.6
|
15.9
|
1.0
|
HB1
|
A:ALA80
|
4.6
|
15.9
|
1.0
|
HD13
|
A:ILE30
|
4.6
|
17.7
|
1.0
|
CG
|
A:HIS58
|
4.6
|
22.8
|
1.0
|
SG
|
A:CYS41
|
4.7
|
20.2
|
1.0
|
CG2
|
A:ILE30
|
4.7
|
17.8
|
1.0
|
N
|
A:CYS38
|
4.7
|
23.9
|
1.0
|
HG23
|
A:ILE36
|
4.7
|
25.2
|
1.0
|
SG
|
A:CYS76
|
4.8
|
14.9
|
1.0
|
HG
|
A:CYS76
|
4.9
|
15.0
|
0.0
|
HB3
|
A:HIS58
|
4.9
|
21.4
|
1.0
|
N
|
A:CYS35
|
4.9
|
18.6
|
1.0
|
ND1
|
A:HIS58
|
4.9
|
23.0
|
1.0
|
N
|
A:HIS58
|
5.0
|
21.4
|
1.0
|
SG
|
A:CYS38
|
5.0
|
22.3
|
1.0
|
HD1
|
A:HIS58
|
5.0
|
23.0
|
0.0
|
C
|
A:ILE36
|
5.0
|
23.4
|
1.0
|
|
Iron binding site 6 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 6 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:20.2
occ:1.00
|
FE2
|
A:SF4502
|
0.0
|
20.2
|
1.0
|
S1
|
A:SF4502
|
2.3
|
19.7
|
1.0
|
S3
|
A:SF4502
|
2.3
|
18.1
|
1.0
|
S4
|
A:SF4502
|
2.3
|
18.7
|
1.0
|
SG
|
A:CYS38
|
2.3
|
22.3
|
1.0
|
FE4
|
A:SF4502
|
2.7
|
16.3
|
1.0
|
FE3
|
A:SF4502
|
2.7
|
18.6
|
1.0
|
FE1
|
A:SF4502
|
2.7
|
17.8
|
1.0
|
H
|
A:CYS38
|
2.8
|
24.0
|
1.0
|
H
|
A:ASP39
|
3.1
|
23.0
|
1.0
|
HG
|
A:CYS38
|
3.1
|
22.3
|
0.0
|
H
|
A:THR40
|
3.4
|
23.2
|
1.0
|
N
|
A:CYS38
|
3.5
|
23.9
|
1.0
|
HD2
|
A:PRO77
|
3.5
|
17.9
|
1.0
|
CB
|
A:CYS38
|
3.7
|
23.2
|
1.0
|
N
|
A:ASP39
|
3.7
|
22.9
|
1.0
|
S2
|
A:SF4502
|
3.9
|
17.3
|
1.0
|
HB3
|
A:CYS38
|
3.9
|
23.2
|
1.0
|
CA
|
A:CYS38
|
4.0
|
24.0
|
1.0
|
H
|
A:CYS41
|
4.0
|
19.7
|
1.0
|
H
|
A:GLY37
|
4.0
|
23.4
|
1.0
|
HB
|
A:THR40
|
4.0
|
23.3
|
1.0
|
HG23
|
A:ILE36
|
4.0
|
25.2
|
1.0
|
N
|
A:THR40
|
4.2
|
23.0
|
1.0
|
C
|
A:CYS38
|
4.2
|
21.9
|
1.0
|
H
|
A:ILE36
|
4.3
|
23.4
|
1.0
|
HG2
|
A:GLU78
|
4.3
|
18.5
|
1.0
|
HG2
|
A:PRO77
|
4.4
|
18.1
|
1.0
|
CD
|
A:PRO77
|
4.4
|
18.1
|
1.0
|
N
|
A:GLY37
|
4.5
|
23.0
|
1.0
|
HB2
|
A:CYS38
|
4.5
|
23.2
|
1.0
|
C
|
A:GLY37
|
4.5
|
24.4
|
1.0
|
HG22
|
A:ILE36
|
4.6
|
25.3
|
1.0
|
SG
|
A:CYS76
|
4.7
|
14.9
|
1.0
|
HA2
|
A:GLY37
|
4.7
|
24.0
|
1.0
|
SG
|
A:CYS41
|
4.7
|
20.2
|
1.0
|
SG
|
A:CYS35
|
4.7
|
21.3
|
1.0
|
CA
|
A:ASP39
|
4.7
|
24.2
|
1.0
|
HA
|
A:CYS76
|
4.7
|
16.8
|
1.0
|
HG3
|
A:GLU78
|
4.7
|
18.6
|
1.0
|
HD3
|
A:PRO77
|
4.7
|
17.9
|
1.0
|
CG2
|
A:ILE36
|
4.8
|
25.3
|
1.0
|
HA
|
A:ASP39
|
4.8
|
24.3
|
1.0
|
CG
|
A:PRO77
|
4.8
|
18.5
|
1.0
|
CA
|
A:GLY37
|
4.8
|
24.2
|
1.0
|
CB
|
A:THR40
|
4.8
|
23.5
|
1.0
|
HG3
|
A:PRO77
|
4.9
|
18.1
|
1.0
|
HG
|
A:CYS41
|
4.9
|
20.2
|
0.0
|
N
|
A:CYS41
|
4.9
|
19.4
|
1.0
|
C
|
A:ASP39
|
4.9
|
24.8
|
1.0
|
HA
|
A:CYS38
|
4.9
|
23.4
|
1.0
|
HB3
|
A:CYS41
|
4.9
|
19.9
|
1.0
|
N
|
A:ILE36
|
5.0
|
23.6
|
1.0
|
CG
|
A:GLU78
|
5.0
|
18.9
|
1.0
|
HA
|
A:CYS35
|
5.0
|
19.7
|
1.0
|
|
Iron binding site 7 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 7 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:18.6
occ:1.00
|
FE3
|
A:SF4502
|
0.0
|
18.6
|
1.0
|
HG
|
A:CYS41
|
2.2
|
20.2
|
0.0
|
S1
|
A:SF4502
|
2.2
|
19.7
|
1.0
|
SG
|
A:CYS41
|
2.3
|
20.2
|
1.0
|
S2
|
A:SF4502
|
2.3
|
17.3
|
1.0
|
S4
|
A:SF4502
|
2.3
|
18.7
|
1.0
|
FE4
|
A:SF4502
|
2.7
|
16.3
|
1.0
|
FE1
|
A:SF4502
|
2.7
|
17.8
|
1.0
|
FE2
|
A:SF4502
|
2.7
|
20.2
|
1.0
|
HB3
|
A:CYS41
|
2.8
|
19.9
|
1.0
|
H
|
A:CYS41
|
3.1
|
19.7
|
1.0
|
CB
|
A:CYS41
|
3.1
|
19.9
|
1.0
|
HD12
|
A:ILE81
|
3.6
|
16.5
|
1.0
|
HB2
|
A:CYS41
|
3.8
|
19.8
|
1.0
|
N
|
A:CYS41
|
3.9
|
19.4
|
1.0
|
S3
|
A:SF4502
|
3.9
|
18.1
|
1.0
|
HB2
|
A:HIS58
|
3.9
|
21.4
|
1.0
|
H
|
A:ASP39
|
4.1
|
23.0
|
1.0
|
CA
|
A:CYS41
|
4.1
|
19.5
|
1.0
|
HD13
|
A:ILE30
|
4.2
|
17.7
|
1.0
|
HD2
|
A:HIS58
|
4.2
|
23.6
|
1.0
|
H
|
A:THR40
|
4.3
|
23.2
|
1.0
|
CD2
|
A:HIS58
|
4.4
|
23.4
|
1.0
|
H
|
A:SER42
|
4.5
|
21.2
|
1.0
|
CD1
|
A:ILE81
|
4.5
|
17.0
|
1.0
|
CB
|
A:HIS58
|
4.5
|
20.9
|
1.0
|
CG
|
A:HIS58
|
4.6
|
22.8
|
1.0
|
HB3
|
A:HIS58
|
4.6
|
21.4
|
1.0
|
HB2
|
A:CYS76
|
4.6
|
16.3
|
1.0
|
HA
|
A:ASP39
|
4.6
|
24.3
|
1.0
|
N
|
A:THR40
|
4.6
|
23.0
|
1.0
|
SG
|
A:CYS35
|
4.6
|
21.3
|
1.0
|
HG21
|
A:ILE50
|
4.7
|
19.1
|
1.0
|
SG
|
A:CYS38
|
4.7
|
22.3
|
1.0
|
HA
|
A:CYS76
|
4.7
|
16.8
|
1.0
|
HB
|
A:THR40
|
4.7
|
23.3
|
1.0
|
N
|
A:ASP39
|
4.7
|
22.9
|
1.0
|
SG
|
A:CYS76
|
4.7
|
14.9
|
1.0
|
HA
|
A:CYS41
|
4.8
|
19.7
|
1.0
|
HD11
|
A:ILE81
|
4.8
|
16.5
|
1.0
|
HD2
|
A:PRO77
|
4.8
|
17.9
|
1.0
|
HG13
|
A:ILE81
|
4.8
|
15.8
|
1.0
|
HG
|
A:CYS35
|
4.9
|
21.3
|
0.0
|
HD13
|
A:ILE50
|
4.9
|
22.2
|
1.0
|
H
|
A:CYS38
|
4.9
|
24.0
|
1.0
|
|
Iron binding site 8 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 8 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:16.3
occ:1.00
|
FE4
|
A:SF4502
|
0.0
|
16.3
|
1.0
|
S1
|
A:SF4502
|
2.2
|
19.7
|
1.0
|
S2
|
A:SF4502
|
2.3
|
17.3
|
1.0
|
SG
|
A:CYS76
|
2.3
|
14.9
|
1.0
|
S3
|
A:SF4502
|
2.3
|
18.1
|
1.0
|
FE3
|
A:SF4502
|
2.7
|
18.6
|
1.0
|
FE2
|
A:SF4502
|
2.7
|
20.2
|
1.0
|
FE1
|
A:SF4502
|
2.7
|
17.8
|
1.0
|
HG
|
A:CYS76
|
2.7
|
15.0
|
0.0
|
HB2
|
A:ALA80
|
3.1
|
15.9
|
1.0
|
HB2
|
A:CYS76
|
3.3
|
16.3
|
1.0
|
HD2
|
A:PRO77
|
3.4
|
17.9
|
1.0
|
CB
|
A:CYS76
|
3.4
|
16.7
|
1.0
|
HA
|
A:CYS76
|
3.6
|
16.8
|
1.0
|
HB2
|
A:GLU78
|
3.8
|
17.5
|
1.0
|
HG13
|
A:ILE81
|
3.8
|
15.8
|
1.0
|
HD12
|
A:ILE81
|
3.8
|
16.5
|
1.0
|
S4
|
A:SF4502
|
3.9
|
18.7
|
1.0
|
CA
|
A:CYS76
|
4.0
|
16.4
|
1.0
|
CB
|
A:ALA80
|
4.0
|
15.9
|
1.0
|
H
|
A:GLU78
|
4.0
|
17.2
|
1.0
|
HB1
|
A:ALA80
|
4.1
|
15.9
|
1.0
|
HB3
|
A:CYS41
|
4.2
|
19.9
|
1.0
|
H
|
A:ALA80
|
4.2
|
16.0
|
1.0
|
HB3
|
A:CYS76
|
4.2
|
16.3
|
1.0
|
CD
|
A:PRO77
|
4.3
|
18.1
|
1.0
|
HG2
|
A:GLU78
|
4.3
|
18.5
|
1.0
|
HA
|
A:CYS35
|
4.3
|
19.7
|
1.0
|
HG
|
A:CYS41
|
4.4
|
20.2
|
0.0
|
CD1
|
A:ILE81
|
4.5
|
17.0
|
1.0
|
HB3
|
A:ALA80
|
4.5
|
15.9
|
1.0
|
HD11
|
A:ILE81
|
4.5
|
16.5
|
1.0
|
CG1
|
A:ILE81
|
4.5
|
15.4
|
1.0
|
C
|
A:CYS76
|
4.6
|
16.5
|
1.0
|
CB
|
A:GLU78
|
4.6
|
16.9
|
1.0
|
SG
|
A:CYS38
|
4.6
|
22.3
|
1.0
|
H
|
A:CYS41
|
4.7
|
19.7
|
1.0
|
N
|
A:PRO77
|
4.7
|
16.8
|
1.0
|
HG3
|
A:GLU78
|
4.7
|
18.6
|
1.0
|
SG
|
A:CYS41
|
4.8
|
20.2
|
1.0
|
H
|
A:ILE36
|
4.8
|
23.4
|
1.0
|
HD3
|
A:PRO77
|
4.8
|
17.9
|
1.0
|
CG
|
A:GLU78
|
4.8
|
18.9
|
1.0
|
HG12
|
A:ILE81
|
4.8
|
15.8
|
1.0
|
N
|
A:GLU78
|
4.8
|
17.3
|
1.0
|
HG2
|
A:PRO77
|
4.9
|
18.1
|
1.0
|
SG
|
A:CYS35
|
4.9
|
21.3
|
1.0
|
HG22
|
A:ILE30
|
4.9
|
18.2
|
1.0
|
HG
|
A:CYS38
|
4.9
|
22.3
|
0.0
|
N
|
A:ALA80
|
4.9
|
15.8
|
1.0
|
CB
|
A:CYS41
|
4.9
|
19.9
|
1.0
|
|
Iron binding site 9 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 9 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:12.4
occ:1.00
|
FE1
|
A:SF4503
|
0.0
|
12.4
|
1.0
|
HG
|
A:CYS234
|
2.0
|
11.6
|
0.0
|
SG
|
A:CYS234
|
2.2
|
11.6
|
1.0
|
S2
|
A:SF4503
|
2.3
|
11.6
|
1.0
|
S4
|
A:SF4503
|
2.3
|
11.3
|
1.0
|
S3
|
A:SF4503
|
2.3
|
11.5
|
1.0
|
FE2
|
A:SF4503
|
2.6
|
12.3
|
1.0
|
FE3
|
A:SF4503
|
2.7
|
11.8
|
1.0
|
FE4
|
A:SF4503
|
2.7
|
12.2
|
1.0
|
HB2
|
A:CYS234
|
3.1
|
11.3
|
1.0
|
CB
|
A:CYS234
|
3.3
|
11.3
|
1.0
|
HB2
|
A:ALA236
|
3.7
|
10.4
|
1.0
|
S1
|
A:SF4503
|
3.7
|
13.0
|
1.0
|
HD2
|
A:PRO180
|
3.7
|
12.8
|
1.0
|
O
|
A:HOH643
|
3.8
|
14.0
|
1.0
|
HG2
|
A:LYS237
|
3.9
|
11.1
|
1.0
|
HB3
|
A:CYS234
|
3.9
|
11.3
|
1.0
|
HG2
|
A:PRO180
|
4.0
|
12.8
|
1.0
|
HA
|
A:CYS234
|
4.0
|
11.5
|
1.0
|
O3
|
A:402504
|
4.1
|
14.5
|
1.0
|
CA
|
A:CYS234
|
4.2
|
11.2
|
1.0
|
HE2
|
A:LYS237
|
4.3
|
10.4
|
1.0
|
H
|
A:ALA236
|
4.3
|
10.7
|
1.0
|
HG
|
A:CYS378
|
4.4
|
14.2
|
0.0
|
C3
|
A:402504
|
4.5
|
13.1
|
1.0
|
H
|
A:GLY181
|
4.5
|
11.9
|
1.0
|
CD
|
A:PRO180
|
4.6
|
12.9
|
1.0
|
H
|
A:LYS237
|
4.6
|
11.5
|
1.0
|
CB
|
A:ALA236
|
4.6
|
10.3
|
1.0
|
SG
|
A:CYS179
|
4.6
|
9.7
|
1.0
|
CG
|
A:PRO180
|
4.7
|
12.7
|
1.0
|
SG
|
A:CYS378
|
4.7
|
14.2
|
1.0
|
HG2
|
A:PRO233
|
4.7
|
11.3
|
1.0
|
SG
|
A:CYS382
|
4.7
|
13.3
|
1.0
|
HA
|
A:CYS382
|
4.8
|
12.1
|
1.0
|
CG
|
A:LYS237
|
4.8
|
11.0
|
1.0
|
H
|
A:GLY386
|
4.9
|
13.7
|
1.0
|
HB1
|
A:ALA236
|
4.9
|
10.4
|
1.0
|
HG3
|
A:PRO180
|
4.9
|
12.8
|
1.0
|
HA
|
A:CYS179
|
4.9
|
12.4
|
1.0
|
HA3
|
A:GLY385
|
4.9
|
13.1
|
1.0
|
HG3
|
A:LYS237
|
5.0
|
11.1
|
1.0
|
H
|
A:ILE235
|
5.0
|
11.3
|
1.0
|
|
Iron binding site 10 out
of 14 in 8ryh
Go back to
Iron Binding Sites List in 8ryh
Iron binding site 10 out
of 14 in the Desulfovibrio Desulfuricans [Fefe]-Hydrogenase Variant with Both Subunits Linked By A Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica
 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 Linker Peptide Derived From A Group A1 Type [Fefe]-Hydrogenase of Veillonella Atypica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:12.3
occ:1.00
|
FE2
|
A:SF4503
|
0.0
|
12.3
|
1.0
|
S1
|
A:SF4503
|
2.2
|
13.0
|
1.0
|
HG
|
A:CYS378
|
2.3
|
14.2
|
0.0
|
S3
|
A:SF4503
|
2.3
|
11.5
|
1.0
|
SG
|
A:CYS378
|
2.3
|
14.2
|
1.0
|
S4
|
A:SF4503
|
2.4
|
11.3
|
1.0
|
FE1
|
A:SF4503
|
2.6
|
12.4
|
1.0
|
FE3
|
A:SF4503
|
2.7
|
11.8
|
1.0
|
FE4
|
A:SF4503
|
2.8
|
12.2
|
1.0
|
HB2
|
A:CYS378
|
3.0
|
12.0
|
1.0
|
CB
|
A:CYS378
|
3.2
|
11.4
|
1.0
|
H
|
A:CYS378
|
3.3
|
11.8
|
1.0
|
HA2
|
A:GLY385
|
3.6
|
13.2
|
1.0
|
N
|
A:CYS378
|
3.8
|
11.5
|
1.0
|
HB2
|
A:ALA377
|
3.8
|
12.9
|
1.0
|
HA
|
A:CYS382
|
3.8
|
12.1
|
1.0
|
S2
|
A:SF4503
|
3.8
|
11.6
|
1.0
|
HB3
|
A:CYS378
|
4.0
|
12.0
|
1.0
|
O
|
A:HOH643
|
4.1
|
14.0
|
1.0
|
CA
|
A:CYS378
|
4.1
|
12.1
|
1.0
|
HA3
|
A:GLY385
|
4.1
|
13.1
|
1.0
|
H
|
A:GLY386
|
4.2
|
13.7
|
1.0
|
H
|
A:ALA377
|
4.3
|
12.5
|
1.0
|
CA
|
A:GLY385
|
4.3
|
12.5
|
1.0
|
SG
|
A:CYS234
|
4.4
|
11.6
|
1.0
|
HB2
|
A:CYS69
|
4.6
|
13.3
|
1.0
|
HG
|
A:CYS234
|
4.6
|
11.6
|
0.0
|
HA
|
A:CYS378
|
4.6
|
12.1
|
1.0
|
C
|
A:ALA377
|
4.7
|
12.1
|
1.0
|
CB
|
A:ALA377
|
4.7
|
12.9
|
1.0
|
SG
|
A:CYS179
|
4.7
|
9.7
|
1.0
|
HE22
|
A:GLN71
|
4.7
|
24.1
|
1.0
|
HG
|
A:CYS179
|
4.7
|
9.7
|
0.0
|
N
|
A:ALA377
|
4.7
|
12.0
|
1.0
|
CA
|
A:CYS382
|
4.8
|
11.8
|
1.0
|
HA
|
A:CYS69
|
4.9
|
13.3
|
1.0
|
HB2
|
A:CYS234
|
4.9
|
11.3
|
1.0
|
SG
|
A:CYS382
|
4.9
|
13.3
|
1.0
|
CA
|
A:ALA377
|
4.9
|
13.2
|
1.0
|
HB3
|
A:MET376
|
5.0
|
13.3
|
1.0
|
O
|
A:GLY381
|
5.0
|
12.8
|
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 09:44:25 2025
|