Iron in PDB 6g7r: Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
Enzymatic activity of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
All present enzymatic activity of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8:
1.12.99.6;
Protein crystallography data
The structure of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8, PDB code: 6g7r
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)
|
67.89 /
1.20
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.068,
97.814,
183.210,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
11.1 /
13.3
|
Other elements in 6g7r:
The structure of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8
(pdb code 6g7r). 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8, PDB code: 6g7r:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 1 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:7.7
occ:1.00
|
FE1
|
S:SF4401
|
0.0
|
7.7
|
1.0
|
|
SG
|
S:CYS215
|
2.3
|
8.1
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
S3
|
S:SF4401
|
2.3
|
7.7
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
FE3
|
S:SF4401
|
2.7
|
7.8
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
7.6
|
1.0
|
|
FE2
|
S:SF4401
|
2.8
|
7.4
|
1.0
|
|
H
|
S:LEU216
|
3.0
|
7.2
|
1.0
|
|
HB2
|
S:PHE196
|
3.4
|
9.2
|
1.0
|
|
CB
|
S:CYS215
|
3.4
|
8.5
|
1.0
|
|
HB2
|
S:CYS215
|
3.5
|
8.4
|
1.0
|
|
H
|
S:TYR217
|
3.6
|
7.2
|
1.0
|
|
HA
|
S:CYS215
|
3.6
|
7.3
|
1.0
|
|
N
|
S:LEU216
|
3.8
|
7.3
|
1.0
|
|
HD1
|
S:PHE196
|
3.8
|
9.4
|
1.0
|
|
HB2
|
S:TYR217
|
3.8
|
8.4
|
1.0
|
|
HB2
|
S:ARG192
|
3.9
|
7.9
|
1.0
|
|
CA
|
S:CYS215
|
3.9
|
7.2
|
1.0
|
|
S1
|
S:SF4401
|
3.9
|
7.8
|
1.0
|
|
N
|
S:TYR217
|
4.2
|
7.2
|
1.0
|
|
HB3
|
S:CYS215
|
4.3
|
8.3
|
1.0
|
|
C
|
S:CYS215
|
4.3
|
7.7
|
1.0
|
|
CB
|
S:PHE196
|
4.4
|
9.3
|
1.0
|
|
HE1
|
S:HIS187
|
4.4
|
8.7
|
1.0
|
|
CD1
|
S:PHE196
|
4.4
|
9.3
|
1.0
|
|
ND1
|
S:HIS187
|
4.5
|
8.4
|
1.0
|
|
HB3
|
S:ARG192
|
4.5
|
7.9
|
1.0
|
|
HB2
|
S:LEU216
|
4.6
|
7.5
|
1.0
|
|
HB3
|
S:CYS221
|
4.6
|
7.3
|
1.0
|
|
CB
|
S:TYR217
|
4.6
|
8.4
|
1.0
|
|
CB
|
S:ARG192
|
4.7
|
7.8
|
1.0
|
|
O
|
S:ARG192
|
4.7
|
7.8
|
1.0
|
|
HA
|
S:TYR217
|
4.8
|
7.5
|
1.0
|
|
CA
|
S:LEU216
|
4.8
|
7.0
|
1.0
|
|
HB3
|
S:TYR217
|
4.8
|
8.4
|
1.0
|
|
CG
|
S:PHE196
|
4.8
|
9.1
|
1.0
|
|
HB3
|
S:PHE196
|
4.8
|
9.3
|
1.0
|
|
C
|
S:LEU216
|
4.8
|
7.8
|
1.0
|
|
HA
|
S:ARG193
|
4.8
|
8.0
|
1.0
|
|
CE1
|
S:HIS187
|
4.8
|
8.9
|
1.0
|
|
CA
|
S:TYR217
|
4.8
|
7.5
|
1.0
|
|
SG
|
S:CYS190
|
4.9
|
7.8
|
1.0
|
|
H
|
S:PHE196
|
4.9
|
8.7
|
1.0
|
|
HD2
|
S:ARG193
|
4.9
|
10.2
|
1.0
|
|
SG
|
S:CYS221
|
4.9
|
7.4
|
1.0
|
|
C
|
S:ARG192
|
5.0
|
8.1
|
1.0
|
|
Iron binding site 2 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 2 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:7.4
occ:1.00
|
FE2
|
S:SF4401
|
0.0
|
7.4
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
SG
|
S:CYS221
|
2.3
|
7.4
|
1.0
|
|
S1
|
S:SF4401
|
2.3
|
7.8
|
1.0
|
|
S3
|
S:SF4401
|
2.3
|
7.7
|
1.0
|
|
FE3
|
S:SF4401
|
2.7
|
7.8
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
7.6
|
1.0
|
|
FE1
|
S:SF4401
|
2.8
|
7.7
|
1.0
|
|
HB3
|
S:CYS221
|
3.1
|
7.3
|
1.0
|
|
CB
|
S:CYS221
|
3.2
|
7.3
|
1.0
|
|
HB2
|
S:CYS221
|
3.5
|
7.3
|
1.0
|
|
HD3
|
S:PRO224
|
3.5
|
8.2
|
1.0
|
|
HD13
|
S:ILE243
|
3.6
|
9.1
|
1.0
|
|
HD12
|
S:ILE243
|
3.6
|
8.8
|
1.0
|
|
HA3
|
S:GLY223
|
3.8
|
8.3
|
1.0
|
|
H
|
S:GLY223
|
3.8
|
7.8
|
1.0
|
|
HG12
|
S:ILE243
|
3.8
|
8.0
|
1.0
|
|
S2
|
S:SF4401
|
3.9
|
8.1
|
1.0
|
|
H
|
S:LEU216
|
4.0
|
7.2
|
1.0
|
|
CD1
|
S:ILE243
|
4.0
|
9.0
|
1.0
|
|
HB2
|
S:LEU216
|
4.0
|
7.5
|
1.0
|
|
CG1
|
S:ILE243
|
4.5
|
8.0
|
1.0
|
|
HG22
|
S:ILE243
|
4.5
|
7.8
|
1.0
|
|
CD
|
S:PRO224
|
4.5
|
8.3
|
1.0
|
|
N
|
S:GLY223
|
4.5
|
7.8
|
1.0
|
|
H
|
S:CYS249
|
4.5
|
7.0
|
1.0
|
|
CA
|
S:GLY223
|
4.6
|
8.4
|
1.0
|
|
CA
|
S:CYS221
|
4.6
|
6.8
|
1.0
|
|
HA
|
S:TYR217
|
4.6
|
7.5
|
1.0
|
|
ND1
|
S:HIS187
|
4.6
|
8.4
|
1.0
|
|
SG
|
S:CYS215
|
4.7
|
8.1
|
1.0
|
|
H
|
S:TYR217
|
4.7
|
7.2
|
1.0
|
|
HB2
|
S:HIS187
|
4.7
|
7.7
|
1.0
|
|
N
|
S:TYR217
|
4.8
|
7.2
|
1.0
|
|
SG
|
S:CYS190
|
4.8
|
7.8
|
1.0
|
|
HG3
|
S:PRO224
|
4.8
|
9.1
|
1.0
|
|
HB2
|
S:TYR217
|
4.8
|
8.4
|
1.0
|
|
N
|
S:LEU216
|
4.8
|
7.3
|
1.0
|
|
HD11
|
S:ILE243
|
4.9
|
8.8
|
1.0
|
|
CB
|
S:LEU216
|
4.9
|
7.5
|
1.0
|
|
C
|
S:CYS221
|
4.9
|
7.6
|
1.0
|
|
HD2
|
S:PRO224
|
4.9
|
8.2
|
1.0
|
|
HG21
|
S:ILE186
|
4.9
|
9.1
|
1.0
|
|
C
|
S:LEU216
|
4.9
|
7.8
|
1.0
|
|
HA2
|
S:GLY248
|
5.0
|
7.3
|
1.0
|
|
HA
|
S:CYS221
|
5.0
|
7.0
|
1.0
|
|
Iron binding site 3 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 3 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:7.8
occ:1.00
|
FE3
|
S:SF4401
|
0.0
|
7.8
|
1.0
|
|
ND1
|
S:HIS187
|
2.1
|
8.4
|
1.0
|
|
S1
|
S:SF4401
|
2.3
|
7.8
|
1.0
|
|
S4
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
FE4
|
S:SF4401
|
2.7
|
7.6
|
1.0
|
|
FE1
|
S:SF4401
|
2.7
|
7.7
|
1.0
|
|
FE2
|
S:SF4401
|
2.7
|
7.4
|
1.0
|
|
CE1
|
S:HIS187
|
3.0
|
8.9
|
1.0
|
|
HE1
|
S:HIS187
|
3.1
|
8.7
|
1.0
|
|
CG
|
S:HIS187
|
3.2
|
8.1
|
1.0
|
|
HB2
|
S:HIS187
|
3.3
|
7.7
|
1.0
|
|
HA
|
S:HIS187
|
3.4
|
7.6
|
1.0
|
|
HG3
|
S:PRO224
|
3.6
|
9.1
|
1.0
|
|
CB
|
S:HIS187
|
3.6
|
7.5
|
1.0
|
|
HD3
|
S:PRO224
|
3.6
|
8.2
|
1.0
|
|
HD3
|
S:ARG193
|
3.8
|
10.4
|
1.0
|
|
S3
|
S:SF4401
|
3.9
|
7.7
|
1.0
|
|
HD2
|
S:ARG193
|
4.0
|
10.2
|
1.0
|
|
CA
|
S:HIS187
|
4.0
|
7.7
|
1.0
|
|
HB3
|
S:CYS190
|
4.0
|
7.7
|
1.0
|
|
NE2
|
S:HIS187
|
4.1
|
8.8
|
1.0
|
|
CD2
|
S:HIS187
|
4.2
|
8.5
|
1.0
|
|
HA3
|
S:GLY223
|
4.3
|
8.3
|
1.0
|
|
CG
|
S:PRO224
|
4.3
|
9.1
|
1.0
|
|
HG2
|
S:ARG193
|
4.4
|
10.2
|
1.0
|
|
CD
|
S:PRO224
|
4.4
|
8.3
|
1.0
|
|
CD
|
S:ARG193
|
4.4
|
10.1
|
1.0
|
|
HB2
|
S:CYS190
|
4.4
|
7.8
|
1.0
|
|
HB2
|
S:PHE196
|
4.4
|
9.2
|
1.0
|
|
CB
|
S:CYS190
|
4.6
|
7.8
|
1.0
|
|
HB3
|
S:HIS187
|
4.6
|
7.6
|
1.0
|
|
HD1
|
S:PHE196
|
4.6
|
9.4
|
1.0
|
|
SG
|
S:CYS215
|
4.6
|
8.1
|
1.0
|
|
SG
|
S:CYS190
|
4.7
|
7.8
|
1.0
|
|
HG2
|
S:PRO224
|
4.7
|
8.8
|
1.0
|
|
SG
|
S:CYS221
|
4.8
|
7.4
|
1.0
|
|
CD1
|
S:PHE196
|
4.8
|
9.3
|
1.0
|
|
O
|
S:HIS187
|
4.8
|
9.3
|
1.0
|
|
N
|
S:PRO224
|
4.9
|
7.6
|
1.0
|
|
HE2
|
S:HIS187
|
4.9
|
8.9
|
0.0
|
|
HB2
|
S:TYR217
|
4.9
|
8.4
|
1.0
|
|
CG
|
S:ARG193
|
4.9
|
10.5
|
1.0
|
|
HA
|
S:ARG193
|
5.0
|
8.0
|
1.0
|
|
Iron binding site 4 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 4 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe401
b:7.6
occ:1.00
|
FE4
|
S:SF4401
|
0.0
|
7.6
|
1.0
|
|
SG
|
S:CYS190
|
2.3
|
7.8
|
1.0
|
|
S2
|
S:SF4401
|
2.3
|
8.1
|
1.0
|
|
S3
|
S:SF4401
|
2.3
|
7.7
|
1.0
|
|
S1
|
S:SF4401
|
2.3
|
7.8
|
1.0
|
|
FE3
|
S:SF4401
|
2.7
|
7.8
|
1.0
|
|
FE2
|
S:SF4401
|
2.7
|
7.4
|
1.0
|
|
FE1
|
S:SF4401
|
2.7
|
7.7
|
1.0
|
|
HB3
|
S:CYS190
|
3.0
|
7.7
|
1.0
|
|
CB
|
S:CYS190
|
3.1
|
7.8
|
1.0
|
|
HB2
|
S:ARG192
|
3.2
|
7.9
|
1.0
|
|
HB2
|
S:CYS190
|
3.3
|
7.8
|
1.0
|
|
HD13
|
S:ILE243
|
3.4
|
9.1
|
1.0
|
|
HG22
|
S:ILE243
|
3.4
|
7.8
|
1.0
|
|
H
|
S:ARG192
|
3.9
|
7.5
|
1.0
|
|
S4
|
S:SF4401
|
3.9
|
8.1
|
1.0
|
|
HA
|
S:HIS187
|
4.1
|
7.6
|
1.0
|
|
CB
|
S:ARG192
|
4.2
|
7.8
|
1.0
|
|
CD1
|
S:ILE243
|
4.3
|
9.0
|
1.0
|
|
HG2
|
S:ARG193
|
4.3
|
10.2
|
1.0
|
|
CG2
|
S:ILE243
|
4.4
|
7.8
|
1.0
|
|
HD12
|
S:ILE243
|
4.4
|
8.8
|
1.0
|
|
HG12
|
S:ILE243
|
4.5
|
8.0
|
1.0
|
|
ND1
|
S:HIS187
|
4.5
|
8.4
|
1.0
|
|
HG23
|
S:ILE243
|
4.6
|
7.9
|
1.0
|
|
CA
|
S:CYS190
|
4.6
|
7.1
|
1.0
|
|
H
|
S:LEU216
|
4.6
|
7.2
|
1.0
|
|
HB3
|
S:ARG192
|
4.6
|
7.9
|
1.0
|
|
HD2
|
S:ARG192
|
4.6
|
8.3
|
1.0
|
|
HG21
|
S:ILE186
|
4.7
|
9.1
|
1.0
|
|
N
|
S:ARG192
|
4.7
|
7.5
|
1.0
|
|
C
|
S:ARG192
|
4.7
|
8.1
|
1.0
|
|
CA
|
S:ARG192
|
4.7
|
8.5
|
1.0
|
|
SG
|
S:CYS221
|
4.8
|
7.4
|
1.0
|
|
N
|
S:ARG193
|
4.8
|
7.5
|
1.0
|
|
CG1
|
S:ILE243
|
4.9
|
8.0
|
1.0
|
|
HG3
|
S:ARG192
|
4.9
|
8.4
|
1.0
|
|
HA
|
S:ARG193
|
4.9
|
8.0
|
1.0
|
|
HA
|
S:CYS215
|
4.9
|
7.3
|
1.0
|
|
HG21
|
S:ILE243
|
4.9
|
7.8
|
1.0
|
|
HD11
|
S:ILE243
|
4.9
|
8.8
|
1.0
|
|
SG
|
S:CYS215
|
4.9
|
8.1
|
1.0
|
|
HA
|
S:CYS190
|
4.9
|
7.1
|
1.0
|
|
H
|
S:ARG193
|
4.9
|
7.6
|
1.0
|
|
C
|
S:CYS190
|
5.0
|
7.1
|
1.0
|
|
Iron binding site 5 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 5 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:8.2
occ:1.00
|
FE1
|
S:F3S402
|
0.0
|
8.2
|
1.0
|
|
S1
|
S:F3S402
|
2.2
|
8.4
|
1.0
|
|
S2
|
S:F3S402
|
2.3
|
8.7
|
1.0
|
|
SG
|
S:CYS252
|
2.3
|
8.9
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
8.0
|
1.0
|
|
FE4
|
S:F3S402
|
2.7
|
7.8
|
1.0
|
|
FE3
|
S:F3S402
|
2.7
|
8.1
|
1.0
|
|
H
|
S:CYS252
|
3.0
|
7.5
|
1.0
|
|
HB3
|
S:CYS252
|
3.3
|
8.4
|
1.0
|
|
CB
|
S:CYS252
|
3.4
|
8.3
|
1.0
|
|
N
|
S:CYS252
|
3.8
|
7.4
|
1.0
|
|
O
|
L:HOH969
|
3.8
|
10.8
|
1.0
|
|
HD22
|
S:ASN228
|
3.9
|
8.3
|
0.0
|
|
S4
|
S:F3S402
|
3.9
|
8.9
|
1.0
|
|
O
|
S:HOH585
|
4.0
|
8.8
|
1.0
|
|
H
|
S:ALA253
|
4.0
|
8.1
|
1.0
|
|
CA
|
S:CYS252
|
4.1
|
7.7
|
1.0
|
|
HG2
|
S:PRO242
|
4.1
|
7.9
|
1.0
|
|
HB2
|
S:CYS252
|
4.2
|
8.1
|
1.0
|
|
H
|
S:CYS149
|
4.4
|
6.7
|
1.0
|
|
H
|
S:LEU250
|
4.4
|
7.2
|
1.0
|
|
HE3
|
L:LYS226
|
4.5
|
9.8
|
1.0
|
|
H
|
S:GLY251
|
4.5
|
7.4
|
1.0
|
|
N
|
S:ALA253
|
4.5
|
8.1
|
1.0
|
|
O
|
L:HOH998
|
4.5
|
10.4
|
1.0
|
|
C
|
S:CYS252
|
4.5
|
7.4
|
1.0
|
|
ND2
|
S:ASN228
|
4.6
|
8.3
|
1.0
|
|
SG
|
S:CYS230
|
4.7
|
8.1
|
1.0
|
|
HD21
|
S:ASN228
|
4.7
|
8.3
|
0.0
|
|
HG22
|
S:THR226
|
4.7
|
7.9
|
1.0
|
|
SG
|
S:CYS249
|
4.7
|
7.8
|
1.0
|
|
HD2
|
L:LYS226
|
4.8
|
9.4
|
1.0
|
|
HZ1
|
L:LYS226
|
4.8
|
11.6
|
1.0
|
|
HB2
|
S:LEU250
|
4.8
|
8.1
|
1.0
|
|
HB2
|
S:ALA253
|
4.8
|
9.9
|
1.0
|
|
HA2
|
S:GLY148
|
4.8
|
6.4
|
1.0
|
|
HD3
|
L:LYS226
|
4.9
|
9.5
|
1.0
|
|
HZ2
|
S:TRP235
|
4.9
|
7.6
|
1.0
|
|
C
|
S:GLY251
|
4.9
|
7.2
|
1.0
|
|
HA
|
S:CYS252
|
4.9
|
7.9
|
1.0
|
|
Iron binding site 6 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 6 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:8.1
occ:1.00
|
FE3
|
S:F3S402
|
0.0
|
8.1
|
1.0
|
|
S4
|
S:F3S402
|
2.3
|
8.9
|
1.0
|
|
S1
|
S:F3S402
|
2.3
|
8.4
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
8.0
|
1.0
|
|
SG
|
S:CYS230
|
2.3
|
8.1
|
1.0
|
|
FE1
|
S:F3S402
|
2.7
|
8.2
|
1.0
|
|
FE4
|
S:F3S402
|
2.7
|
7.8
|
1.0
|
|
HB2
|
S:CYS230
|
3.2
|
7.8
|
1.0
|
|
CB
|
S:CYS230
|
3.3
|
7.5
|
1.0
|
|
HB3
|
S:CYS230
|
3.4
|
7.5
|
1.0
|
|
HD22
|
S:ASN228
|
3.5
|
8.3
|
0.0
|
|
HE1
|
S:TRP235
|
3.5
|
7.1
|
1.0
|
|
HD12
|
S:ILE186
|
3.5
|
10.7
|
1.0
|
|
HG2
|
S:PRO242
|
3.8
|
7.9
|
1.0
|
|
HD2
|
S:PRO242
|
3.8
|
7.3
|
1.0
|
|
ND2
|
S:ASN228
|
3.9
|
8.3
|
1.0
|
|
S2
|
S:F3S402
|
4.0
|
8.7
|
1.0
|
|
HB3
|
S:ASN228
|
4.1
|
7.5
|
1.0
|
|
HD11
|
S:ILE186
|
4.1
|
10.7
|
1.0
|
|
HG13
|
S:ILE186
|
4.2
|
10.3
|
1.0
|
|
CD1
|
S:ILE186
|
4.2
|
10.9
|
1.0
|
|
HD21
|
S:ASN228
|
4.2
|
8.3
|
0.0
|
|
O
|
S:HOH585
|
4.3
|
8.8
|
1.0
|
|
NE1
|
S:TRP235
|
4.3
|
7.5
|
1.0
|
|
H
|
S:CYS230
|
4.5
|
7.6
|
1.0
|
|
CD
|
S:PRO242
|
4.5
|
7.2
|
1.0
|
|
CG
|
S:PRO242
|
4.5
|
8.0
|
1.0
|
|
CG
|
S:ASN228
|
4.6
|
7.4
|
1.0
|
|
HD2
|
S:PHE241
|
4.6
|
8.4
|
1.0
|
|
CA
|
S:CYS230
|
4.7
|
7.3
|
1.0
|
|
CB
|
S:ASN228
|
4.7
|
7.7
|
1.0
|
|
HZ2
|
S:TRP235
|
4.7
|
7.6
|
1.0
|
|
HD3
|
S:PRO242
|
4.7
|
7.2
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
8.9
|
1.0
|
|
CG1
|
S:ILE186
|
4.8
|
10.3
|
1.0
|
|
SG
|
S:CYS249
|
4.8
|
7.8
|
1.0
|
|
HD2
|
L:LYS226
|
4.8
|
9.4
|
1.0
|
|
HB2
|
S:ASN228
|
4.9
|
7.8
|
1.0
|
|
HB2
|
S:PHE241
|
5.0
|
7.2
|
1.0
|
|
Iron binding site 7 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 7 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe402
b:7.8
occ:1.00
|
FE4
|
S:F3S402
|
0.0
|
7.8
|
1.0
|
|
S4
|
S:F3S402
|
2.2
|
8.9
|
1.0
|
|
S2
|
S:F3S402
|
2.3
|
8.7
|
1.0
|
|
SG
|
S:CYS249
|
2.3
|
7.8
|
1.0
|
|
S3
|
S:F3S402
|
2.3
|
8.0
|
1.0
|
|
FE1
|
S:F3S402
|
2.7
|
8.2
|
1.0
|
|
FE3
|
S:F3S402
|
2.7
|
8.1
|
1.0
|
|
HA
|
S:CYS249
|
3.2
|
7.0
|
1.0
|
|
H
|
S:GLY251
|
3.2
|
7.4
|
1.0
|
|
CB
|
S:CYS249
|
3.2
|
7.6
|
1.0
|
|
HB2
|
S:CYS249
|
3.3
|
7.6
|
1.0
|
|
H
|
S:LEU250
|
3.5
|
7.2
|
1.0
|
|
H
|
S:CYS252
|
3.5
|
7.5
|
1.0
|
|
HG22
|
S:THR226
|
3.7
|
7.9
|
1.0
|
|
CA
|
S:CYS249
|
3.7
|
6.7
|
1.0
|
|
HG13
|
S:ILE186
|
3.7
|
10.3
|
1.0
|
|
S1
|
S:F3S402
|
3.9
|
8.4
|
1.0
|
|
HG2
|
S:PRO242
|
3.9
|
7.9
|
1.0
|
|
N
|
S:LEU250
|
4.1
|
7.1
|
1.0
|
|
HB3
|
S:CYS249
|
4.1
|
7.3
|
1.0
|
|
N
|
S:GLY251
|
4.2
|
7.3
|
1.0
|
|
C
|
S:CYS249
|
4.3
|
6.8
|
1.0
|
|
N
|
S:CYS252
|
4.4
|
7.4
|
1.0
|
|
HA2
|
S:GLY251
|
4.5
|
7.9
|
1.0
|
|
HB2
|
S:PRO242
|
4.5
|
7.5
|
1.0
|
|
HD12
|
S:ILE186
|
4.6
|
10.7
|
1.0
|
|
CG2
|
S:THR226
|
4.6
|
7.8
|
1.0
|
|
CG1
|
S:ILE186
|
4.6
|
10.3
|
1.0
|
|
HG22
|
S:ILE186
|
4.7
|
9.1
|
1.0
|
|
HG21
|
S:THR226
|
4.7
|
7.9
|
1.0
|
|
CA
|
S:GLY251
|
4.8
|
8.0
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
8.9
|
1.0
|
|
CG
|
S:PRO242
|
4.8
|
8.0
|
1.0
|
|
HD11
|
S:ILE186
|
4.8
|
10.7
|
1.0
|
|
HG1
|
S:THR226
|
4.8
|
7.8
|
0.0
|
|
H
|
S:ALA253
|
4.9
|
8.1
|
1.0
|
|
SG
|
S:CYS230
|
4.9
|
8.1
|
1.0
|
|
HD2
|
S:PRO242
|
4.9
|
7.3
|
1.0
|
|
CD1
|
S:ILE186
|
4.9
|
10.9
|
1.0
|
|
HB3
|
S:CYS252
|
4.9
|
8.4
|
1.0
|
|
N
|
S:CYS249
|
4.9
|
7.2
|
1.0
|
|
HD22
|
S:ASN228
|
5.0
|
8.3
|
0.0
|
|
HB
|
S:THR226
|
5.0
|
7.9
|
1.0
|
|
HB2
|
S:CYS230
|
5.0
|
7.8
|
1.0
|
|
Iron binding site 8 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 8 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:7.8
occ:1.00
|
FE1
|
S:SF3403
|
0.0
|
7.8
|
1.0
|
|
SG
|
S:CYS115
|
2.3
|
8.8
|
1.0
|
|
S1
|
S:SF3403
|
2.3
|
7.6
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
7.9
|
1.0
|
|
S2
|
S:SF3403
|
2.3
|
7.9
|
1.0
|
|
FE4
|
S:SF3403
|
2.6
|
8.0
|
1.0
|
|
FE3
|
S:SF3403
|
2.8
|
7.7
|
1.0
|
|
FE7
|
S:SF3403
|
2.8
|
8.3
|
1.0
|
|
HB2
|
S:CYS115
|
3.1
|
8.9
|
1.0
|
|
H
|
S:CYS115
|
3.3
|
7.0
|
1.0
|
|
CB
|
S:CYS115
|
3.3
|
9.1
|
1.0
|
|
H
|
S:CYS17
|
3.6
|
8.9
|
1.0
|
|
O
|
S:HOH532
|
3.9
|
10.1
|
1.0
|
|
HB3
|
S:CYS120
|
4.0
|
7.4
|
1.0
|
|
SG
|
S:CYS19
|
4.0
|
7.8
|
1.0
|
|
N
|
S:CYS115
|
4.0
|
6.9
|
1.0
|
|
HA
|
S:GLU16
|
4.0
|
9.3
|
1.0
|
|
HB3
|
S:CYS115
|
4.1
|
8.7
|
1.0
|
|
CA
|
S:CYS115
|
4.2
|
7.5
|
1.0
|
|
O
|
S:HOH592
|
4.2
|
8.7
|
1.0
|
|
HB2
|
S:CYS120
|
4.4
|
7.4
|
1.0
|
|
SG
|
S:CYS120
|
4.4
|
8.0
|
1.0
|
|
HB2
|
S:GLU16
|
4.4
|
11.2
|
1.0
|
|
CB
|
S:CYS120
|
4.4
|
7.4
|
1.0
|
|
HA
|
S:CYS115
|
4.5
|
7.7
|
1.0
|
|
HB3
|
S:GLU16
|
4.5
|
11.8
|
1.0
|
|
HA2
|
S:GLY77
|
4.6
|
7.8
|
1.0
|
|
N
|
S:CYS17
|
4.6
|
8.9
|
1.0
|
|
SG
|
S:CYS20
|
4.6
|
8.2
|
1.0
|
|
HE21
|
S:GLN122
|
4.6
|
8.4
|
0.0
|
|
H
|
S:GLY77
|
4.7
|
7.7
|
1.0
|
|
SG
|
S:CYS17
|
4.7
|
7.8
|
1.0
|
|
SG
|
S:CYS149
|
4.8
|
7.7
|
1.0
|
|
CA
|
S:GLU16
|
4.8
|
9.2
|
1.0
|
|
CB
|
S:GLU16
|
4.8
|
12.1
|
1.0
|
|
HB3
|
S:CYS17
|
4.9
|
7.8
|
1.0
|
|
H
|
S:CYS19
|
4.9
|
7.4
|
1.0
|
|
HA3
|
S:GLY113
|
4.9
|
7.4
|
1.0
|
|
H
|
S:THR18
|
5.0
|
7.8
|
1.0
|
|
Iron binding site 9 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 9 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:7.7
occ:1.00
|
FE3
|
S:SF3403
|
0.0
|
7.7
|
1.0
|
|
SG
|
S:CYS149
|
2.3
|
7.7
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
7.9
|
1.0
|
|
S1
|
S:SF3403
|
2.3
|
7.6
|
1.0
|
|
SG
|
S:CYS120
|
2.4
|
8.0
|
1.0
|
|
FE1
|
S:SF3403
|
2.8
|
7.8
|
1.0
|
|
HB2
|
S:CYS149
|
3.2
|
7.5
|
1.0
|
|
CB
|
S:CYS149
|
3.3
|
7.4
|
1.0
|
|
HA
|
S:CYS149
|
3.4
|
6.8
|
1.0
|
|
CB
|
S:CYS120
|
3.5
|
7.4
|
1.0
|
|
HB3
|
S:CYS120
|
3.5
|
7.4
|
1.0
|
|
FE4
|
S:SF3403
|
3.6
|
8.0
|
1.0
|
|
HB2
|
S:CYS120
|
3.6
|
7.4
|
1.0
|
|
HB
|
S:THR114
|
3.7
|
8.0
|
1.0
|
|
H
|
S:CYS115
|
3.8
|
7.0
|
1.0
|
|
HG2
|
L:ARG74
|
3.8
|
7.4
|
1.0
|
|
CA
|
S:CYS149
|
3.9
|
6.6
|
1.0
|
|
HG3
|
L:ARG74
|
4.0
|
7.7
|
1.0
|
|
FE7
|
S:SF3403
|
4.0
|
8.3
|
1.0
|
|
SG
|
S:CYS115
|
4.0
|
8.8
|
1.0
|
|
H
|
S:VAL121
|
4.0
|
7.0
|
1.0
|
|
SG
|
S:CYS19
|
4.1
|
7.8
|
1.0
|
|
HB3
|
S:CYS149
|
4.1
|
7.3
|
1.0
|
|
HE
|
L:ARG74
|
4.3
|
7.4
|
1.0
|
|
HZ2
|
S:TRP258
|
4.4
|
8.0
|
1.0
|
|
CG
|
L:ARG74
|
4.4
|
7.5
|
1.0
|
|
N
|
S:CYS115
|
4.4
|
6.9
|
1.0
|
|
H
|
S:THR114
|
4.5
|
7.1
|
1.0
|
|
CB
|
S:THR114
|
4.6
|
8.0
|
1.0
|
|
S2
|
S:SF3403
|
4.7
|
7.9
|
1.0
|
|
HE1
|
S:TRP258
|
4.7
|
7.9
|
1.0
|
|
C
|
S:CYS149
|
4.8
|
6.4
|
1.0
|
|
CA
|
S:CYS120
|
4.9
|
7.0
|
1.0
|
|
O
|
S:GLY148
|
4.9
|
7.6
|
1.0
|
|
HD2
|
L:HIS229
|
4.9
|
7.6
|
1.0
|
|
HB
|
S:VAL121
|
4.9
|
8.1
|
1.0
|
|
HG11
|
S:VAL121
|
4.9
|
8.8
|
1.0
|
|
N
|
S:VAL121
|
4.9
|
7.0
|
1.0
|
|
HB3
|
L:ARG74
|
4.9
|
7.8
|
1.0
|
|
Iron binding site 10 out
of 24 in 6g7r
Go back to
Iron Binding Sites List in 6g7r
Iron binding site 10 out
of 24 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8
 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe403
b:8.0
occ:1.00
|
FE4
|
S:SF3403
|
0.0
|
8.0
|
1.0
|
|
SG
|
S:CYS17
|
2.3
|
7.8
|
1.0
|
|
S3
|
S:SF3403
|
2.3
|
7.9
|
1.0
|
|
S2
|
S:SF3403
|
2.3
|
7.9
|
1.0
|
|
SG
|
S:CYS19
|
2.3
|
7.8
|
1.0
|
|
FE1
|
S:SF3403
|
2.6
|
7.8
|
1.0
|
|
H
|
S:CYS19
|
2.8
|
7.4
|
1.0
|
|
FE7
|
S:SF3403
|
2.8
|
8.3
|
1.0
|
|
H
|
S:CYS17
|
2.8
|
8.9
|
1.0
|
|
HB3
|
S:CYS17
|
3.3
|
7.8
|
1.0
|
|
CB
|
S:CYS17
|
3.4
|
7.7
|
1.0
|
|
HE2
|
L:HIS229
|
3.4
|
9.1
|
0.0
|
|
HB3
|
S:CYS19
|
3.4
|
7.5
|
1.0
|
|
CB
|
S:CYS19
|
3.4
|
7.6
|
1.0
|
|
FE3
|
S:SF3403
|
3.6
|
7.7
|
1.0
|
|
N
|
S:CYS19
|
3.7
|
7.3
|
1.0
|
|
N
|
S:CYS17
|
3.7
|
8.9
|
1.0
|
|
S1
|
S:SF3403
|
3.7
|
7.6
|
1.0
|
|
H
|
S:THR18
|
3.9
|
7.8
|
1.0
|
|
CA
|
S:CYS17
|
3.9
|
7.8
|
1.0
|
|
CA
|
S:CYS19
|
4.1
|
7.4
|
1.0
|
|
HG3
|
L:ARG74
|
4.1
|
7.7
|
1.0
|
|
H
|
S:CYS20
|
4.2
|
6.8
|
1.0
|
|
NE2
|
L:HIS229
|
4.2
|
9.0
|
1.0
|
|
HB2
|
S:CYS17
|
4.2
|
7.7
|
1.0
|
|
N
|
S:THR18
|
4.2
|
7.6
|
1.0
|
|
HB2
|
S:CYS19
|
4.3
|
7.8
|
1.0
|
|
C
|
S:CYS17
|
4.3
|
8.0
|
1.0
|
|
SG
|
S:CYS149
|
4.5
|
7.7
|
1.0
|
|
O
|
S:HOH592
|
4.5
|
8.7
|
1.0
|
|
HD2
|
L:HIS229
|
4.6
|
7.6
|
1.0
|
|
HB2
|
S:GLU16
|
4.6
|
11.2
|
1.0
|
|
SG
|
S:CYS115
|
4.6
|
8.8
|
1.0
|
|
HA
|
S:GLU16
|
4.7
|
9.3
|
1.0
|
|
N
|
S:CYS20
|
4.8
|
6.7
|
1.0
|
|
CD2
|
L:HIS229
|
4.8
|
7.7
|
1.0
|
|
C
|
S:THR18
|
4.8
|
7.6
|
1.0
|
|
HA
|
S:CYS19
|
4.9
|
7.4
|
1.0
|
|
HA
|
S:CYS17
|
4.9
|
7.8
|
1.0
|
|
C
|
S:CYS19
|
4.9
|
6.7
|
1.0
|
|
C
|
S:GLU16
|
4.9
|
9.3
|
1.0
|
|
HB3
|
L:ARG74
|
4.9
|
7.8
|
1.0
|
|
HA3
|
L:GLY77
|
4.9
|
8.6
|
1.0
|
|
CG
|
L:ARG74
|
5.0
|
7.5
|
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 19:12:02 2024
|
