Iron in PDB 6fpi: Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q:
1.12.99.6;
Protein crystallography data
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q, PDB code: 6fpi
was solved by
S.B.Carr,
F.A.Armstrong,
R.M.Evans,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
83.51 /
1.50
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.820,
97.730,
183.200,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.5 /
16.7
|
Other elements in 6fpi:
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Iron atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
(pdb code 6fpi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q, PDB code: 6fpi:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 1 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:14.0
occ:1.00
|
FE1
|
S:SF4401
|
0.0
|
14.0
|
1.0
|
|
SG
|
S:CYS215
|
2.2
|
14.0
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
14.6
|
1.0
|
|
S3
|
S:SF4401
|
2.3
|
13.7
|
1.0
|
|
FE3
|
S:SF4401
|
2.7
|
14.2
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
13.6
|
1.0
|
|
FE2
|
S:SF4401
|
2.8
|
13.9
|
1.0
|
|
HG
|
S:CYS215
|
2.8
|
14.3
|
0.0
|
|
H
|
S:LEU216
|
3.0
|
13.2
|
1.0
|
|
HB2
|
S:PHE196
|
3.3
|
16.1
|
1.0
|
|
CB
|
S:CYS215
|
3.4
|
14.7
|
1.0
|
|
HB2
|
S:CYS215
|
3.5
|
14.5
|
1.0
|
|
H
|
S:TYR217
|
3.5
|
14.7
|
1.0
|
|
HA
|
S:CYS215
|
3.6
|
14.6
|
1.0
|
|
HG
|
S:CYS190
|
3.7
|
13.4
|
0.0
|
|
HG
|
S:CYS221
|
3.8
|
13.0
|
0.0
|
|
N
|
S:LEU216
|
3.8
|
12.5
|
1.0
|
|
HD2
|
S:PHE196
|
3.8
|
16.5
|
1.0
|
|
HD1
|
S:HIS187
|
3.8
|
13.0
|
0.0
|
|
HB2
|
S:TYR217
|
3.8
|
16.4
|
1.0
|
|
CA
|
S:CYS215
|
3.9
|
14.6
|
1.0
|
|
S1
|
S:SF4401
|
4.0
|
13.3
|
1.0
|
|
HB2
|
S:ARG192
|
4.0
|
14.1
|
1.0
|
|
N
|
S:TYR217
|
4.2
|
15.0
|
1.0
|
|
HB3
|
S:CYS215
|
4.2
|
14.5
|
1.0
|
|
HE1
|
S:HIS187
|
4.2
|
13.8
|
1.0
|
|
CB
|
S:PHE196
|
4.3
|
16.2
|
1.0
|
|
C
|
S:CYS215
|
4.3
|
14.5
|
1.0
|
|
CD2
|
S:PHE196
|
4.4
|
16.1
|
1.0
|
|
HB3
|
S:ARG192
|
4.5
|
14.1
|
1.0
|
|
ND1
|
S:HIS187
|
4.5
|
13.0
|
1.0
|
|
HB3
|
S:CYS221
|
4.5
|
13.5
|
1.0
|
|
CB
|
S:TYR217
|
4.5
|
16.3
|
1.0
|
|
HB3
|
S:PHE196
|
4.6
|
16.1
|
1.0
|
|
HB2
|
S:LEU216
|
4.7
|
14.4
|
1.0
|
|
HB3
|
S:TYR217
|
4.7
|
16.4
|
1.0
|
|
CB
|
S:ARG192
|
4.7
|
13.8
|
1.0
|
|
O
|
S:ARG192
|
4.7
|
14.7
|
1.0
|
|
HA
|
S:ARG193
|
4.7
|
15.2
|
1.0
|
|
CE1
|
S:HIS187
|
4.7
|
13.8
|
1.0
|
|
CG
|
S:PHE196
|
4.7
|
16.1
|
1.0
|
|
HA
|
S:TYR217
|
4.7
|
15.1
|
1.0
|
|
CA
|
S:TYR217
|
4.8
|
15.0
|
1.0
|
|
CA
|
S:LEU216
|
4.8
|
13.5
|
1.0
|
|
H
|
S:PHE196
|
4.8
|
16.2
|
1.0
|
|
C
|
S:LEU216
|
4.8
|
13.8
|
1.0
|
|
SG
|
S:CYS221
|
4.9
|
13.0
|
1.0
|
|
SG
|
S:CYS190
|
4.9
|
13.2
|
1.0
|
|
C
|
S:ARG192
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 2 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 2 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:13.9
occ:1.00
|
FE2
|
S:SF4401
|
0.0
|
13.9
|
1.0
|
|
HG
|
S:CYS221
|
1.2
|
13.0
|
0.0
|
|
S1
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
SG
|
S:CYS221
|
2.3
|
13.0
|
1.0
|
|
S3
|
S:SF4401
|
2.3
|
13.7
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
14.6
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
13.6
|
1.0
|
|
FE3
|
S:SF4401
|
2.8
|
14.2
|
1.0
|
|
FE1
|
S:SF4401
|
2.8
|
14.0
|
1.0
|
|
HB3
|
S:CYS221
|
3.0
|
13.5
|
1.0
|
|
CB
|
S:CYS221
|
3.2
|
13.7
|
1.0
|
|
HD12
|
S:ILE243
|
3.4
|
12.9
|
1.0
|
|
HD3
|
S:PRO224
|
3.5
|
14.9
|
1.0
|
|
HB2
|
S:CYS221
|
3.5
|
13.5
|
1.0
|
|
HG
|
S:CYS190
|
3.5
|
13.4
|
0.0
|
|
HD13
|
S:ILE243
|
3.7
|
12.9
|
1.0
|
|
HA3
|
S:GLY223
|
3.7
|
13.8
|
1.0
|
|
HD1
|
S:HIS187
|
3.7
|
13.0
|
0.0
|
|
H
|
S:GLY223
|
3.8
|
14.1
|
1.0
|
|
HG12
|
S:ILE243
|
3.8
|
12.5
|
1.0
|
|
H
|
S:LEU216
|
3.9
|
13.2
|
1.0
|
|
S2
|
S:SF4401
|
3.9
|
13.3
|
1.0
|
|
CD1
|
S:ILE243
|
4.0
|
13.2
|
1.0
|
|
HB2
|
S:LEU216
|
4.0
|
14.4
|
1.0
|
|
HG22
|
S:ILE243
|
4.4
|
13.2
|
1.0
|
|
CD
|
S:PRO224
|
4.4
|
14.7
|
1.0
|
|
CG1
|
S:ILE243
|
4.4
|
12.3
|
1.0
|
|
N
|
S:GLY223
|
4.5
|
13.9
|
1.0
|
|
CA
|
S:GLY223
|
4.5
|
13.8
|
1.0
|
|
ND1
|
S:HIS187
|
4.6
|
13.0
|
1.0
|
|
CA
|
S:CYS221
|
4.6
|
13.6
|
1.0
|
|
H
|
S:CYS249
|
4.6
|
13.2
|
1.0
|
|
HA
|
S:TYR217
|
4.6
|
15.1
|
1.0
|
|
SG
|
S:CYS215
|
4.7
|
14.0
|
1.0
|
|
H
|
S:TYR217
|
4.7
|
14.7
|
1.0
|
|
N
|
S:TYR217
|
4.8
|
15.0
|
1.0
|
|
SG
|
S:CYS190
|
4.8
|
13.2
|
1.0
|
|
HG3
|
S:PRO224
|
4.8
|
15.7
|
1.0
|
|
HD11
|
S:ILE243
|
4.8
|
12.9
|
1.0
|
|
HB2
|
S:TYR217
|
4.8
|
16.4
|
1.0
|
|
N
|
S:LEU216
|
4.8
|
12.5
|
1.0
|
|
HD2
|
S:PRO224
|
4.8
|
14.9
|
1.0
|
|
C
|
S:CYS221
|
4.8
|
14.1
|
1.0
|
|
HG21
|
S:ILE186
|
4.9
|
14.9
|
1.0
|
|
HB2
|
S:HIS187
|
4.9
|
14.0
|
1.0
|
|
CB
|
S:LEU216
|
4.9
|
14.3
|
1.0
|
|
HA
|
S:CYS221
|
5.0
|
13.6
|
1.0
|
|
HA2
|
S:GLY248
|
5.0
|
12.2
|
1.0
|
|
C
|
S:LEU216
|
5.0
|
13.8
|
1.0
|
|
O
|
S:CYS221
|
5.0
|
14.7
|
1.0
|
|
Iron binding site 3 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 3 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:14.2
occ:1.00
|
FE3
|
S:SF4401
|
0.0
|
14.2
|
1.0
|
|
HD1
|
S:HIS187
|
1.2
|
13.0
|
0.0
|
|
ND1
|
S:HIS187
|
2.0
|
13.0
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
14.6
|
1.0
|
|
S1
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
FE1
|
S:SF4401
|
2.7
|
14.0
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
13.6
|
1.0
|
|
FE2
|
S:SF4401
|
2.8
|
13.9
|
1.0
|
|
CE1
|
S:HIS187
|
2.8
|
13.8
|
1.0
|
|
HE1
|
S:HIS187
|
2.9
|
13.8
|
1.0
|
|
CG
|
S:HIS187
|
3.2
|
14.1
|
1.0
|
|
HA
|
S:HIS187
|
3.4
|
14.2
|
1.0
|
|
HB2
|
S:HIS187
|
3.4
|
14.0
|
1.0
|
|
HG3
|
S:PRO224
|
3.4
|
15.7
|
1.0
|
|
HD3
|
S:PRO224
|
3.5
|
14.9
|
1.0
|
|
CB
|
S:HIS187
|
3.7
|
14.0
|
1.0
|
|
HG
|
S:CYS190
|
3.7
|
13.4
|
0.0
|
|
HG
|
S:CYS221
|
3.9
|
13.0
|
0.0
|
|
S3
|
S:SF4401
|
3.9
|
13.7
|
1.0
|
|
CA
|
S:HIS187
|
4.0
|
14.0
|
1.0
|
|
NE2
|
S:HIS187
|
4.0
|
14.5
|
1.0
|
|
HB3
|
S:CYS190
|
4.1
|
12.6
|
1.0
|
|
HD3
|
S:ARG193
|
4.1
|
23.0
|
1.0
|
|
CD2
|
S:HIS187
|
4.2
|
16.0
|
1.0
|
|
CG
|
S:PRO224
|
4.2
|
16.0
|
1.0
|
|
CD
|
S:PRO224
|
4.2
|
14.7
|
1.0
|
|
HD2
|
S:ARG193
|
4.3
|
23.0
|
1.0
|
|
HA3
|
S:GLY223
|
4.3
|
13.8
|
1.0
|
|
HB2
|
S:PHE196
|
4.4
|
16.1
|
1.0
|
|
HB2
|
S:CYS190
|
4.4
|
12.6
|
1.0
|
|
HG
|
S:CYS215
|
4.6
|
14.3
|
0.0
|
|
CB
|
S:CYS190
|
4.6
|
12.3
|
1.0
|
|
HG2
|
S:PRO224
|
4.6
|
15.7
|
1.0
|
|
HD2
|
S:PHE196
|
4.6
|
16.5
|
1.0
|
|
HB3
|
S:HIS187
|
4.6
|
14.0
|
1.0
|
|
SG
|
S:CYS215
|
4.6
|
14.0
|
1.0
|
|
CD
|
S:ARG193
|
4.7
|
23.2
|
1.0
|
|
SG
|
S:CYS190
|
4.7
|
13.2
|
1.0
|
|
CD2
|
S:PHE196
|
4.7
|
16.1
|
1.0
|
|
HE2
|
S:HIS187
|
4.8
|
14.6
|
0.0
|
|
N
|
S:PRO224
|
4.8
|
14.4
|
1.0
|
|
O
|
S:HIS187
|
4.8
|
16.4
|
1.0
|
|
SG
|
S:CYS221
|
4.8
|
13.0
|
1.0
|
|
HB2
|
S:TYR217
|
4.8
|
16.4
|
1.0
|
|
HA
|
S:ARG193
|
4.9
|
15.2
|
1.0
|
|
C
|
S:HIS187
|
5.0
|
14.8
|
1.0
|
|
CG
|
S:PHE196
|
5.0
|
16.1
|
1.0
|
|
Iron binding site 4 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 4 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:13.6
occ:1.00
|
FE4
|
S:SF4401
|
0.0
|
13.6
|
1.0
|
|
HG
|
S:CYS190
|
1.1
|
13.4
|
0.0
|
|
S3
|
S:SF4401
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS190
|
2.3
|
13.2
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
S1
|
S:SF4401
|
2.3
|
13.3
|
1.0
|
|
FE2
|
S:SF4401
|
2.7
|
13.9
|
1.0
|
|
FE3
|
S:SF4401
|
2.7
|
14.2
|
1.0
|
|
FE1
|
S:SF4401
|
2.7
|
14.0
|
1.0
|
|
HB3
|
S:CYS190
|
3.0
|
12.6
|
1.0
|
|
CB
|
S:CYS190
|
3.1
|
12.3
|
1.0
|
|
HB2
|
S:ARG192
|
3.2
|
14.1
|
1.0
|
|
HB2
|
S:CYS190
|
3.2
|
12.6
|
1.0
|
|
HG22
|
S:ILE243
|
3.4
|
13.2
|
1.0
|
|
HD13
|
S:ILE243
|
3.5
|
12.9
|
1.0
|
|
HG
|
S:CYS221
|
3.5
|
13.0
|
0.0
|
|
HD1
|
S:HIS187
|
3.7
|
13.0
|
0.0
|
|
S4
|
S:SF4401
|
3.9
|
14.6
|
1.0
|
|
H
|
S:ARG192
|
3.9
|
14.0
|
1.0
|
|
HA
|
S:HIS187
|
4.1
|
14.2
|
1.0
|
|
CB
|
S:ARG192
|
4.1
|
13.8
|
1.0
|
|
CD1
|
S:ILE243
|
4.3
|
13.2
|
1.0
|
|
HD12
|
S:ILE243
|
4.3
|
12.9
|
1.0
|
|
CG2
|
S:ILE243
|
4.4
|
13.6
|
1.0
|
|
ND1
|
S:HIS187
|
4.5
|
13.0
|
1.0
|
|
HG12
|
S:ILE243
|
4.5
|
12.5
|
1.0
|
|
HB3
|
S:ARG192
|
4.5
|
14.1
|
1.0
|
|
H
|
S:LEU216
|
4.6
|
13.2
|
1.0
|
|
CA
|
S:CYS190
|
4.6
|
12.4
|
1.0
|
|
HD2
|
S:ARG192
|
4.6
|
14.8
|
1.0
|
|
C
|
S:ARG192
|
4.7
|
14.6
|
1.0
|
|
HG23
|
S:ILE243
|
4.7
|
13.2
|
1.0
|
|
HG21
|
S:ILE186
|
4.7
|
14.9
|
1.0
|
|
N
|
S:ARG192
|
4.7
|
14.1
|
1.0
|
|
CA
|
S:ARG192
|
4.7
|
14.4
|
1.0
|
|
SG
|
S:CYS221
|
4.8
|
13.0
|
1.0
|
|
HA
|
S:ARG193
|
4.8
|
15.2
|
1.0
|
|
HG21
|
S:ILE243
|
4.8
|
13.2
|
1.0
|
|
N
|
S:ARG193
|
4.8
|
14.1
|
1.0
|
|
CG1
|
S:ILE243
|
4.8
|
12.3
|
1.0
|
|
HA
|
S:CYS190
|
4.9
|
12.7
|
1.0
|
|
HG3
|
S:ARG192
|
4.9
|
14.4
|
1.0
|
|
SG
|
S:CYS215
|
4.9
|
14.0
|
1.0
|
|
HA
|
S:CYS215
|
4.9
|
14.6
|
1.0
|
|
HD11
|
S:ILE243
|
5.0
|
12.9
|
1.0
|
|
Iron binding site 5 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 5 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:14.4
occ:1.00
|
FE1
|
S:F3S402
|
0.0
|
14.4
|
1.0
|
|
S1
|
S:F3S402
|
2.2
|
14.1
|
1.0
|
|
S2
|
S:F3S402
|
2.2
|
13.8
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
13.6
|
1.0
|
|
SG
|
S:CYS252
|
2.3
|
15.0
|
1.0
|
|
FE4
|
S:F3S402
|
2.7
|
13.7
|
1.0
|
|
FE3
|
S:F3S402
|
2.7
|
14.1
|
1.0
|
|
HG
|
S:CYS252
|
2.8
|
15.2
|
0.0
|
|
H
|
S:CYS252
|
3.0
|
12.7
|
1.0
|
|
HB3
|
S:CYS252
|
3.4
|
13.9
|
1.0
|
|
HG
|
S:CYS230
|
3.4
|
13.8
|
0.0
|
|
CB
|
S:CYS252
|
3.4
|
14.1
|
1.0
|
|
O
|
L:HOH953
|
3.8
|
16.4
|
1.0
|
|
HD22
|
S:ASN228
|
3.8
|
13.4
|
0.0
|
|
N
|
S:CYS252
|
3.8
|
12.5
|
1.0
|
|
S4
|
S:F3S402
|
3.9
|
14.8
|
1.0
|
|
O
|
S:HOH578
|
4.0
|
14.0
|
1.0
|
|
CA
|
S:CYS252
|
4.0
|
12.7
|
1.0
|
|
H
|
S:ALA253
|
4.1
|
13.2
|
1.0
|
|
HG2
|
S:PRO242
|
4.1
|
11.9
|
1.0
|
|
HB2
|
S:CYS252
|
4.3
|
13.9
|
1.0
|
|
H
|
S:CYS149
|
4.4
|
11.4
|
1.0
|
|
O
|
L:HOH999
|
4.4
|
18.4
|
1.0
|
|
HE3
|
L:LYS226
|
4.4
|
15.9
|
1.0
|
|
H
|
S:LEU250
|
4.5
|
13.1
|
1.0
|
|
H
|
S:GLY251
|
4.5
|
13.5
|
1.0
|
|
N
|
S:ALA253
|
4.5
|
13.0
|
1.0
|
|
C
|
S:CYS252
|
4.5
|
13.2
|
1.0
|
|
ND2
|
S:ASN228
|
4.6
|
13.4
|
1.0
|
|
SG
|
S:CYS230
|
4.7
|
13.6
|
1.0
|
|
HD21
|
S:ASN228
|
4.7
|
13.4
|
0.0
|
|
HZ1
|
L:LYS226
|
4.7
|
17.0
|
1.0
|
|
SG
|
S:CYS249
|
4.8
|
14.4
|
1.0
|
|
HG22
|
S:THR226
|
4.8
|
14.4
|
1.0
|
|
HD2
|
L:LYS226
|
4.8
|
14.7
|
1.0
|
|
HB1
|
S:ALA253
|
4.8
|
13.9
|
1.0
|
|
HB2
|
S:LEU250
|
4.8
|
13.6
|
1.0
|
|
HD3
|
L:LYS226
|
4.9
|
14.8
|
1.0
|
|
HA2
|
S:GLY148
|
4.9
|
11.9
|
1.0
|
|
HA
|
S:CYS252
|
4.9
|
13.0
|
1.0
|
|
HZ2
|
S:TRP235
|
4.9
|
12.8
|
1.0
|
|
C
|
S:GLY251
|
5.0
|
13.3
|
1.0
|
|
Iron binding site 6 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 6 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:14.1
occ:1.00
|
FE3
|
S:F3S402
|
0.0
|
14.1
|
1.0
|
|
HG
|
S:CYS230
|
1.0
|
13.8
|
0.0
|
|
S4
|
S:F3S402
|
2.2
|
14.8
|
1.0
|
|
S1
|
S:F3S402
|
2.2
|
14.1
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
13.6
|
1.0
|
|
SG
|
S:CYS230
|
2.3
|
13.6
|
1.0
|
|
FE4
|
S:F3S402
|
2.7
|
13.7
|
1.0
|
|
FE1
|
S:F3S402
|
2.7
|
14.4
|
1.0
|
|
HB2
|
S:CYS230
|
3.3
|
13.9
|
1.0
|
|
CB
|
S:CYS230
|
3.3
|
13.7
|
1.0
|
|
HD22
|
S:ASN228
|
3.4
|
13.4
|
0.0
|
|
HB3
|
S:CYS230
|
3.4
|
13.9
|
1.0
|
|
HD12
|
S:ILE186
|
3.5
|
19.1
|
1.0
|
|
HE1
|
S:TRP235
|
3.5
|
13.4
|
1.0
|
|
HG2
|
S:PRO242
|
3.7
|
11.9
|
1.0
|
|
HD2
|
S:PRO242
|
3.8
|
11.9
|
1.0
|
|
S2
|
S:F3S402
|
3.9
|
13.8
|
1.0
|
|
ND2
|
S:ASN228
|
4.0
|
13.4
|
1.0
|
|
HB3
|
S:ASN228
|
4.1
|
13.5
|
1.0
|
|
HG13
|
S:ILE186
|
4.1
|
17.2
|
1.0
|
|
O
|
S:HOH578
|
4.3
|
14.0
|
1.0
|
|
NE1
|
S:TRP235
|
4.3
|
13.9
|
1.0
|
|
HD21
|
S:ASN228
|
4.3
|
13.4
|
0.0
|
|
CD1
|
S:ILE186
|
4.4
|
20.2
|
1.0
|
|
H
|
S:CYS230
|
4.5
|
14.1
|
1.0
|
|
CG
|
S:PRO242
|
4.5
|
11.8
|
1.0
|
|
CD
|
S:PRO242
|
4.5
|
11.8
|
1.0
|
|
HD11
|
S:ILE186
|
4.6
|
19.2
|
1.0
|
|
CG
|
S:ASN228
|
4.6
|
12.5
|
1.0
|
|
HD2
|
S:PHE241
|
4.7
|
14.5
|
1.0
|
|
CA
|
S:CYS230
|
4.7
|
14.7
|
1.0
|
|
CB
|
S:ASN228
|
4.7
|
14.1
|
1.0
|
|
HZ2
|
S:TRP235
|
4.7
|
12.8
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
15.0
|
1.0
|
|
CG1
|
S:ILE186
|
4.8
|
17.2
|
1.0
|
|
HB2
|
S:ASN228
|
4.8
|
13.5
|
1.0
|
|
HD3
|
S:PRO242
|
4.8
|
11.9
|
1.0
|
|
SG
|
S:CYS249
|
4.8
|
14.4
|
1.0
|
|
HD2
|
L:LYS226
|
4.9
|
14.7
|
1.0
|
|
HB2
|
S:PHE241
|
5.0
|
12.5
|
1.0
|
|
Iron binding site 7 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 7 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:13.7
occ:1.00
|
FE4
|
S:F3S402
|
0.0
|
13.7
|
1.0
|
|
S4
|
S:F3S402
|
2.2
|
14.8
|
1.0
|
|
S2
|
S:F3S402
|
2.3
|
13.8
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
13.6
|
1.0
|
|
SG
|
S:CYS249
|
2.4
|
14.4
|
1.0
|
|
FE1
|
S:F3S402
|
2.7
|
14.4
|
1.0
|
|
FE3
|
S:F3S402
|
2.7
|
14.1
|
1.0
|
|
HA
|
S:CYS249
|
3.1
|
13.0
|
1.0
|
|
HG
|
S:CYS249
|
3.1
|
14.5
|
0.0
|
|
H
|
S:GLY251
|
3.3
|
13.5
|
1.0
|
|
CB
|
S:CYS249
|
3.3
|
13.2
|
1.0
|
|
HB2
|
S:CYS249
|
3.3
|
13.3
|
1.0
|
|
H
|
S:CYS252
|
3.5
|
12.7
|
1.0
|
|
H
|
S:LEU250
|
3.5
|
13.1
|
1.0
|
|
CA
|
S:CYS249
|
3.6
|
12.5
|
1.0
|
|
HG
|
S:CYS230
|
3.6
|
13.8
|
0.0
|
|
HG13
|
S:ILE186
|
3.7
|
17.2
|
1.0
|
|
S1
|
S:F3S402
|
3.8
|
14.1
|
1.0
|
|
HG22
|
S:THR226
|
3.9
|
14.4
|
1.0
|
|
HG2
|
S:PRO242
|
3.9
|
11.9
|
1.0
|
|
N
|
S:LEU250
|
4.1
|
13.0
|
1.0
|
|
HB3
|
S:CYS249
|
4.2
|
13.3
|
1.0
|
|
N
|
S:GLY251
|
4.2
|
13.5
|
1.0
|
|
C
|
S:CYS249
|
4.3
|
13.2
|
1.0
|
|
N
|
S:CYS252
|
4.4
|
12.5
|
1.0
|
|
HA2
|
S:GLY251
|
4.5
|
13.3
|
1.0
|
|
HD12
|
S:ILE186
|
4.6
|
19.1
|
1.0
|
|
HB2
|
S:PRO242
|
4.6
|
12.1
|
1.0
|
|
HG21
|
S:THR226
|
4.6
|
14.4
|
1.0
|
|
CG2
|
S:THR226
|
4.7
|
14.6
|
1.0
|
|
CG1
|
S:ILE186
|
4.7
|
17.2
|
1.0
|
|
HG22
|
S:ILE186
|
4.7
|
14.9
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
15.0
|
1.0
|
|
CA
|
S:GLY251
|
4.8
|
13.3
|
1.0
|
|
CG
|
S:PRO242
|
4.8
|
11.8
|
1.0
|
|
HG1
|
S:THR226
|
4.8
|
14.5
|
0.0
|
|
SG
|
S:CYS230
|
4.8
|
13.6
|
1.0
|
|
HD22
|
S:ASN228
|
4.8
|
13.4
|
0.0
|
|
H
|
S:ALA253
|
4.9
|
13.2
|
1.0
|
|
HD2
|
S:PRO242
|
4.9
|
11.9
|
1.0
|
|
N
|
S:CYS249
|
4.9
|
13.6
|
1.0
|
|
O
|
L:HOH999
|
5.0
|
18.4
|
1.0
|
|
HB
|
S:THR226
|
5.0
|
14.0
|
1.0
|
|
HB2
|
S:CYS230
|
5.0
|
13.9
|
1.0
|
|
HB3
|
S:CYS252
|
5.0
|
13.9
|
1.0
|
|
Iron binding site 8 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 8 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:14.2
occ:1.00
|
FE1
|
S:SF3403
|
0.0
|
14.2
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
13.8
|
1.0
|
|
SG
|
S:CYS115
|
2.3
|
14.1
|
1.0
|
|
S1
|
S:SF3403
|
2.3
|
12.7
|
1.0
|
|
S2
|
S:SF3403
|
2.4
|
13.7
|
1.0
|
|
FE4
|
S:SF3403
|
2.6
|
14.1
|
1.0
|
|
FE3
|
S:SF3403
|
2.7
|
13.8
|
1.0
|
|
FE7
|
S:SF3403
|
2.8
|
14.5
|
1.0
|
|
HB2
|
S:CYS115
|
3.1
|
13.9
|
1.0
|
|
H
|
S:CYS115
|
3.3
|
13.3
|
1.0
|
|
CB
|
S:CYS115
|
3.3
|
13.9
|
1.0
|
|
H
|
S:CYS17
|
3.6
|
14.0
|
1.0
|
|
O
|
S:HOH547
|
3.9
|
15.5
|
1.0
|
|
HB3
|
S:CYS120
|
4.0
|
13.4
|
1.0
|
|
HA
|
S:GLU16
|
4.0
|
16.4
|
0.5
|
|
HA
|
S:GLU16
|
4.0
|
16.3
|
0.5
|
|
SG
|
S:CYS19
|
4.1
|
13.4
|
1.0
|
|
HB3
|
S:CYS115
|
4.1
|
13.9
|
1.0
|
|
N
|
S:CYS115
|
4.1
|
13.2
|
1.0
|
|
O
|
S:HOH584
|
4.2
|
13.6
|
1.0
|
|
CA
|
S:CYS115
|
4.2
|
13.7
|
1.0
|
|
HB2
|
S:GLU16
|
4.4
|
18.5
|
0.5
|
|
HB2
|
S:CYS120
|
4.4
|
13.4
|
1.0
|
|
SG
|
S:CYS120
|
4.4
|
13.9
|
1.0
|
|
CB
|
S:CYS120
|
4.4
|
13.3
|
1.0
|
|
HA
|
S:CYS115
|
4.5
|
13.5
|
1.0
|
|
HA2
|
S:GLY77
|
4.6
|
13.9
|
1.0
|
|
N
|
S:CYS17
|
4.6
|
13.6
|
1.0
|
|
SG
|
S:CYS20
|
4.6
|
14.1
|
1.0
|
|
HE21
|
S:GLN122
|
4.6
|
13.8
|
0.0
|
|
H
|
S:GLY77
|
4.7
|
13.8
|
1.0
|
|
HB3
|
S:GLU16
|
4.7
|
18.9
|
0.5
|
|
SG
|
S:CYS17
|
4.7
|
13.9
|
1.0
|
|
HB2
|
S:GLU16
|
4.7
|
18.9
|
0.5
|
|
SG
|
S:CYS149
|
4.8
|
12.8
|
1.0
|
|
CA
|
S:GLU16
|
4.8
|
16.0
|
0.5
|
|
H
|
S:CYS19
|
4.8
|
12.3
|
1.0
|
|
CA
|
S:GLU16
|
4.8
|
15.9
|
0.5
|
|
HB3
|
S:CYS17
|
4.9
|
13.2
|
1.0
|
|
H
|
S:THR18
|
4.9
|
13.5
|
1.0
|
|
CB
|
S:GLU16
|
5.0
|
19.2
|
0.5
|
|
Iron binding site 9 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 9 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:13.8
occ:1.00
|
FE3
|
S:SF3403
|
0.0
|
13.8
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
13.8
|
1.0
|
|
S1
|
S:SF3403
|
2.3
|
12.7
|
1.0
|
|
SG
|
S:CYS149
|
2.3
|
12.8
|
1.0
|
|
SG
|
S:CYS120
|
2.4
|
13.9
|
1.0
|
|
FE1
|
S:SF3403
|
2.7
|
14.2
|
1.0
|
|
HB2
|
S:CYS149
|
3.2
|
11.9
|
1.0
|
|
CB
|
S:CYS149
|
3.4
|
12.1
|
1.0
|
|
HA
|
S:CYS149
|
3.4
|
11.4
|
1.0
|
|
CB
|
S:CYS120
|
3.5
|
13.3
|
1.0
|
|
FE4
|
S:SF3403
|
3.5
|
14.1
|
1.0
|
|
HB3
|
S:CYS120
|
3.5
|
13.4
|
1.0
|
|
HB
|
S:THR114
|
3.6
|
13.4
|
1.0
|
|
HB2
|
S:CYS120
|
3.7
|
13.4
|
1.0
|
|
HG2
|
L:ARG74
|
3.8
|
13.2
|
1.0
|
|
H
|
S:CYS115
|
3.8
|
13.3
|
1.0
|
|
CA
|
S:CYS149
|
4.0
|
10.7
|
1.0
|
|
HG3
|
L:ARG74
|
4.0
|
13.2
|
1.0
|
|
FE7
|
S:SF3403
|
4.0
|
14.5
|
1.0
|
|
SG
|
S:CYS115
|
4.0
|
14.1
|
1.0
|
|
H
|
S:VAL121
|
4.1
|
13.0
|
1.0
|
|
SG
|
S:CYS19
|
4.1
|
13.4
|
1.0
|
|
HB3
|
S:CYS149
|
4.2
|
11.9
|
1.0
|
|
HE
|
L:ARG74
|
4.2
|
13.7
|
1.0
|
|
CG
|
L:ARG74
|
4.4
|
13.0
|
1.0
|
|
HZ2
|
S:TRP258
|
4.4
|
13.7
|
1.0
|
|
N
|
S:CYS115
|
4.5
|
13.2
|
1.0
|
|
H
|
S:THR114
|
4.5
|
12.7
|
1.0
|
|
CB
|
S:THR114
|
4.6
|
13.1
|
1.0
|
|
S2
|
S:SF3403
|
4.7
|
13.7
|
1.0
|
|
HE1
|
S:TRP258
|
4.8
|
14.1
|
1.0
|
|
HG21
|
S:THR114
|
4.8
|
14.3
|
1.0
|
|
C
|
S:CYS149
|
4.8
|
11.9
|
1.0
|
|
HB3
|
L:ARG74
|
4.9
|
13.2
|
1.0
|
|
HD2
|
L:HIS229
|
4.9
|
12.6
|
1.0
|
|
CA
|
S:CYS120
|
4.9
|
13.0
|
1.0
|
|
HB
|
S:VAL121
|
4.9
|
13.9
|
1.0
|
|
O
|
S:GLY148
|
5.0
|
12.5
|
1.0
|
|
N
|
S:VAL121
|
5.0
|
12.6
|
1.0
|
|
Iron binding site 10 out
of 24 in 6fpi
Go back to
Iron Binding Sites List in 6fpi
Iron binding site 10 out
of 24 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:14.1
occ:1.00
|
FE4
|
S:SF3403
|
0.0
|
14.1
|
1.0
|
|
SG
|
S:CYS17
|
2.3
|
13.9
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
13.8
|
1.0
|
|
S2
|
S:SF3403
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS19
|
2.3
|
13.4
|
1.0
|
|
FE1
|
S:SF3403
|
2.6
|
14.2
|
1.0
|
|
H
|
S:CYS19
|
2.7
|
12.3
|
1.0
|
|
FE7
|
S:SF3403
|
2.8
|
14.5
|
1.0
|
|
H
|
S:CYS17
|
2.8
|
14.0
|
1.0
|
|
HB3
|
S:CYS17
|
3.3
|
13.2
|
1.0
|
|
HE2
|
L:HIS229
|
3.3
|
13.6
|
0.0
|
|
CB
|
S:CYS17
|
3.4
|
12.9
|
1.0
|
|
HB3
|
S:CYS19
|
3.4
|
12.6
|
1.0
|
|
CB
|
S:CYS19
|
3.5
|
12.6
|
1.0
|
|
FE3
|
S:SF3403
|
3.5
|
13.8
|
1.0
|
|
N
|
S:CYS19
|
3.6
|
12.2
|
1.0
|
|
N
|
S:CYS17
|
3.7
|
13.6
|
1.0
|
|
S1
|
S:SF3403
|
3.7
|
12.7
|
1.0
|
|
H
|
S:THR18
|
3.9
|
13.5
|
1.0
|
|
CA
|
S:CYS17
|
3.9
|
13.1
|
1.0
|
|
CA
|
S:CYS19
|
4.1
|
11.7
|
1.0
|
|
HG3
|
L:ARG74
|
4.1
|
13.2
|
1.0
|
|
NE2
|
L:HIS229
|
4.2
|
13.5
|
1.0
|
|
N
|
S:THR18
|
4.2
|
12.9
|
1.0
|
|
HB2
|
S:CYS17
|
4.2
|
13.2
|
1.0
|
|
H
|
S:CYS20
|
4.2
|
13.3
|
1.0
|
|
C
|
S:CYS17
|
4.3
|
13.2
|
1.0
|
|
HB2
|
S:CYS19
|
4.3
|
12.6
|
1.0
|
|
SG
|
S:CYS149
|
4.4
|
12.8
|
1.0
|
|
O
|
S:HOH584
|
4.5
|
13.6
|
1.0
|
|
HD2
|
L:HIS229
|
4.6
|
12.6
|
1.0
|
|
SG
|
S:CYS115
|
4.6
|
14.1
|
1.0
|
|
HA
|
S:GLU16
|
4.7
|
16.4
|
0.5
|
|
HA
|
S:GLU16
|
4.7
|
16.3
|
0.5
|
|
N
|
S:CYS20
|
4.8
|
13.3
|
1.0
|
|
C
|
S:THR18
|
4.8
|
13.3
|
1.0
|
|
HB2
|
S:GLU16
|
4.8
|
18.5
|
0.5
|
|
CD2
|
L:HIS229
|
4.8
|
12.5
|
1.0
|
|
HB3
|
L:ARG74
|
4.8
|
13.2
|
1.0
|
|
HB2
|
S:GLU16
|
4.8
|
18.9
|
0.5
|
|
HA
|
S:CYS19
|
4.9
|
12.3
|
1.0
|
|
C
|
S:CYS19
|
4.9
|
13.3
|
1.0
|
|
HA
|
S:CYS17
|
4.9
|
13.2
|
1.0
|
|
C
|
S:GLU16
|
4.9
|
15.9
|
1.0
|
|
HA3
|
L:GLY77
|
4.9
|
14.1
|
1.0
|
|
CG
|
L:ARG74
|
4.9
|
13.0
|
1.0
|
|
Reference:
R.M.Evans,
P.A.Ash,
S.E.Beaton,
E.J.Brooke,
K.A.Vincent,
S.B.Carr,
F.A.Armstrong.
Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Tue Aug 6 18:31:41 2024
|
