Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8, PDB code: 6g7r:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 6g7r
Go back to
Chlorine Binding Sites List in 6g7r
Chlorine binding site 1 out
of 4 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 Chlorine with other atoms in the Cl 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:Cl405
b:13.7
occ:1.00
|
H
|
S:GLY256
|
2.1
|
9.4
|
1.0
|
|
H
|
S:CYS120
|
2.3
|
6.9
|
1.0
|
|
O
|
S:HOH590
|
3.0
|
12.8
|
1.0
|
|
N
|
S:GLY256
|
3.1
|
9.3
|
1.0
|
|
HB2
|
S:TRP118
|
3.1
|
10.7
|
1.0
|
|
O
|
S:HOH683
|
3.1
|
25.6
|
1.0
|
|
HA
|
S:CYS120
|
3.2
|
6.9
|
1.0
|
|
N
|
S:CYS120
|
3.2
|
6.8
|
1.0
|
|
HB3
|
S:TRP118
|
3.2
|
10.8
|
1.0
|
|
HG21
|
S:THR114
|
3.3
|
8.6
|
1.0
|
|
HA2
|
S:GLY256
|
3.4
|
10.0
|
1.0
|
|
HA
|
S:ASN255
|
3.5
|
9.4
|
1.0
|
|
HG23
|
S:THR114
|
3.6
|
8.9
|
1.0
|
|
CB
|
S:TRP118
|
3.7
|
10.7
|
1.0
|
|
HG22
|
S:THR114
|
3.7
|
8.7
|
1.0
|
|
H
|
S:PHE257
|
3.7
|
8.8
|
1.0
|
|
CA
|
S:CYS120
|
3.7
|
7.0
|
1.0
|
|
CG2
|
S:THR114
|
3.7
|
8.9
|
1.0
|
|
CA
|
S:GLY256
|
3.8
|
10.0
|
1.0
|
|
HD1
|
S:TRP258
|
3.8
|
8.4
|
1.0
|
|
HD1
|
S:PHE257
|
4.1
|
8.6
|
1.0
|
|
HA3
|
S:GLY119
|
4.1
|
7.8
|
1.0
|
|
N
|
S:GLY119
|
4.1
|
8.0
|
1.0
|
|
C
|
S:TRP118
|
4.1
|
9.2
|
1.0
|
|
C
|
S:ASN255
|
4.1
|
8.9
|
1.0
|
|
C
|
S:GLY119
|
4.2
|
7.4
|
1.0
|
|
OD1
|
S:ASN255
|
4.2
|
13.1
|
1.0
|
|
CA
|
S:ASN255
|
4.2
|
9.5
|
1.0
|
|
O
|
S:TRP118
|
4.3
|
11.3
|
1.0
|
|
CA
|
S:GLY119
|
4.3
|
7.7
|
1.0
|
|
H
|
S:GLY119
|
4.3
|
8.2
|
1.0
|
|
O
|
S:CYS120
|
4.3
|
7.9
|
1.0
|
|
O
|
S:GLU254
|
4.4
|
9.5
|
1.0
|
|
N
|
S:PHE257
|
4.4
|
8.9
|
1.0
|
|
C
|
S:CYS120
|
4.5
|
7.1
|
1.0
|
|
C
|
S:GLY256
|
4.5
|
9.6
|
1.0
|
|
HB3
|
S:ALA123
|
4.5
|
9.4
|
1.0
|
|
O
|
S:HOH645
|
4.6
|
29.0
|
1.0
|
|
HA3
|
S:GLY256
|
4.6
|
10.1
|
1.0
|
|
CA
|
S:TRP118
|
4.6
|
9.1
|
1.0
|
|
CD1
|
S:TRP258
|
4.6
|
8.6
|
1.0
|
|
H
|
S:TRP258
|
4.6
|
8.0
|
1.0
|
|
CG
|
S:TRP118
|
4.7
|
14.2
|
1.0
|
|
CD1
|
S:PHE257
|
4.7
|
8.4
|
1.0
|
|
HE1
|
S:PHE257
|
4.8
|
9.0
|
1.0
|
|
HB2
|
S:CYS120
|
4.8
|
7.4
|
1.0
|
|
CB
|
S:CYS120
|
4.9
|
7.4
|
1.0
|
|
O
|
S:HOH646
|
4.9
|
30.0
|
1.0
|
|
HE1
|
S:TRP258
|
4.9
|
7.9
|
1.0
|
|
O
|
S:THR114
|
4.9
|
7.6
|
1.0
|
|
HD1
|
S:TRP118
|
4.9
|
16.8
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 6g7r
Go back to
Chlorine Binding Sites List in 6g7r
Chlorine binding site 2 out
of 4 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 Chlorine with other atoms in the Cl 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:Cl406
b:27.5
occ:1.00
|
H
|
S:HIS13
|
2.1
|
8.1
|
1.0
|
|
HA
|
S:ILE12
|
2.8
|
8.2
|
1.0
|
|
O
|
S:HOH557
|
2.9
|
23.4
|
1.0
|
|
HB
|
S:ILE12
|
2.9
|
9.1
|
1.0
|
|
O
|
S:HOH522
|
3.0
|
15.5
|
1.0
|
|
HZ3
|
S:LYS98
|
3.0
|
25.8
|
1.0
|
|
N
|
S:HIS13
|
3.0
|
8.2
|
1.0
|
|
HE1
|
S:TYR44
|
3.1
|
11.8
|
1.0
|
|
HE2
|
S:LYS98
|
3.2
|
19.8
|
1.0
|
|
OD2
|
S:ASP46
|
3.2
|
22.6
|
1.0
|
|
CA
|
S:ILE12
|
3.4
|
7.9
|
1.0
|
|
HD1
|
S:HIS13
|
3.4
|
14.6
|
0.0
|
|
HB2
|
S:HIS13
|
3.4
|
10.5
|
1.0
|
|
HG21
|
S:ILE12
|
3.5
|
10.6
|
1.0
|
|
CB
|
S:ILE12
|
3.6
|
9.1
|
1.0
|
|
NZ
|
S:LYS98
|
3.6
|
27.6
|
1.0
|
|
HZ2
|
S:LYS98
|
3.6
|
24.8
|
1.0
|
|
O
|
S:HOH509
|
3.6
|
34.1
|
1.0
|
|
C
|
S:ILE12
|
3.7
|
8.6
|
1.0
|
|
O
|
S:HIS13
|
3.8
|
9.9
|
1.0
|
|
CG
|
S:ASP46
|
3.8
|
17.4
|
1.0
|
|
CE
|
S:LYS98
|
3.8
|
19.9
|
1.0
|
|
HD3
|
S:LYS98
|
3.9
|
18.1
|
1.0
|
|
CA
|
S:HIS13
|
4.0
|
8.9
|
1.0
|
|
CG2
|
S:ILE12
|
4.0
|
10.8
|
1.0
|
|
HE1
|
L:HIS30
|
4.0
|
17.9
|
1.0
|
|
HE1
|
S:PHE95
|
4.0
|
11.7
|
1.0
|
|
CE1
|
S:TYR44
|
4.0
|
12.7
|
1.0
|
|
CB
|
S:HIS13
|
4.1
|
10.6
|
1.0
|
|
HB2
|
S:ASP46
|
4.2
|
14.7
|
1.0
|
|
ND1
|
S:HIS13
|
4.2
|
14.4
|
1.0
|
|
HH
|
S:TYR44
|
4.2
|
16.1
|
0.0
|
|
OD1
|
S:ASP46
|
4.2
|
21.2
|
1.0
|
|
C
|
S:HIS13
|
4.3
|
8.9
|
1.0
|
|
CD
|
S:LYS98
|
4.4
|
18.7
|
1.0
|
|
HZ1
|
S:LYS98
|
4.4
|
26.1
|
1.0
|
|
HG22
|
S:ILE12
|
4.4
|
10.5
|
1.0
|
|
H
|
S:ASP46
|
4.4
|
10.9
|
1.0
|
|
OH
|
S:TYR44
|
4.5
|
16.0
|
1.0
|
|
O
|
S:TRP11
|
4.5
|
9.5
|
1.0
|
|
HG
|
S:SER90
|
4.6
|
14.8
|
0.0
|
|
CB
|
S:ASP46
|
4.6
|
15.0
|
1.0
|
|
CG
|
S:HIS13
|
4.6
|
12.0
|
1.0
|
|
HE3
|
S:LYS98
|
4.6
|
20.2
|
1.0
|
|
N
|
S:ILE12
|
4.7
|
7.6
|
1.0
|
|
CZ
|
S:TYR44
|
4.7
|
12.2
|
1.0
|
|
HG23
|
S:ILE12
|
4.8
|
10.6
|
1.0
|
|
HG
|
S:SER90
|
4.8
|
22.0
|
0.0
|
|
HA
|
S:HIS13
|
4.8
|
8.9
|
1.0
|
|
CE1
|
S:PHE95
|
4.8
|
12.0
|
1.0
|
|
HD1
|
S:TYR44
|
4.9
|
10.8
|
1.0
|
|
HD1
|
S:PHE95
|
4.9
|
11.0
|
1.0
|
|
CG1
|
S:ILE12
|
4.9
|
9.8
|
1.0
|
|
CE1
|
L:HIS30
|
4.9
|
20.4
|
1.0
|
|
HB3
|
S:HIS13
|
4.9
|
10.2
|
1.0
|
|
O
|
S:ILE12
|
4.9
|
8.6
|
1.0
|
|
CD1
|
S:TYR44
|
4.9
|
11.0
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 6g7r
Go back to
Chlorine Binding Sites List in 6g7r
Chlorine binding site 3 out
of 4 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 Chlorine with other atoms in the Cl 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
|
T:Cl405
b:15.1
occ:1.00
|
H
|
T:GLY256
|
2.1
|
9.7
|
1.0
|
|
H
|
T:CYS120
|
2.3
|
7.7
|
1.0
|
|
O
|
T:HOH634
|
3.0
|
14.0
|
1.0
|
|
O
|
T:HOH707
|
3.1
|
27.0
|
1.0
|
|
N
|
T:GLY256
|
3.1
|
9.4
|
1.0
|
|
HB2
|
T:TRP118
|
3.1
|
12.1
|
1.0
|
|
HA
|
T:CYS120
|
3.1
|
7.7
|
1.0
|
|
N
|
T:CYS120
|
3.2
|
7.7
|
1.0
|
|
HB3
|
T:TRP118
|
3.2
|
11.7
|
1.0
|
|
HA2
|
T:GLY256
|
3.4
|
10.2
|
1.0
|
|
HG21
|
T:THR114
|
3.4
|
9.5
|
1.0
|
|
HA
|
T:ASN255
|
3.5
|
9.7
|
1.0
|
|
HG23
|
T:THR114
|
3.6
|
9.7
|
1.0
|
|
CB
|
T:TRP118
|
3.6
|
12.1
|
1.0
|
|
CA
|
T:CYS120
|
3.7
|
7.6
|
1.0
|
|
HG22
|
T:THR114
|
3.7
|
9.4
|
1.0
|
|
H
|
T:PHE257
|
3.7
|
9.2
|
1.0
|
|
CA
|
T:GLY256
|
3.8
|
10.2
|
1.0
|
|
HD1
|
T:TRP258
|
3.8
|
8.6
|
1.0
|
|
CG2
|
T:THR114
|
3.8
|
9.7
|
1.0
|
|
N
|
T:GLY119
|
4.1
|
9.1
|
1.0
|
|
HD1
|
T:PHE257
|
4.1
|
9.2
|
1.0
|
|
C
|
T:TRP118
|
4.1
|
10.0
|
1.0
|
|
HA3
|
T:GLY119
|
4.1
|
8.9
|
1.0
|
|
C
|
T:ASN255
|
4.1
|
10.1
|
1.0
|
|
C
|
T:GLY119
|
4.2
|
8.0
|
1.0
|
|
OD1
|
T:ASN255
|
4.2
|
14.1
|
1.0
|
|
CA
|
T:ASN255
|
4.2
|
9.7
|
1.0
|
|
O
|
T:TRP118
|
4.3
|
13.2
|
1.0
|
|
CA
|
T:GLY119
|
4.3
|
8.9
|
1.0
|
|
H
|
T:GLY119
|
4.3
|
9.2
|
1.0
|
|
O
|
T:CYS120
|
4.4
|
8.0
|
1.0
|
|
O
|
T:GLU254
|
4.4
|
9.8
|
1.0
|
|
N
|
T:PHE257
|
4.4
|
9.0
|
1.0
|
|
HB3
|
T:ALA123
|
4.5
|
10.1
|
1.0
|
|
C
|
T:CYS120
|
4.5
|
7.5
|
1.0
|
|
C
|
T:GLY256
|
4.5
|
9.3
|
1.0
|
|
HA3
|
T:GLY256
|
4.6
|
10.0
|
1.0
|
|
CA
|
T:TRP118
|
4.6
|
10.6
|
1.0
|
|
H
|
T:TRP258
|
4.6
|
8.6
|
1.0
|
|
CD1
|
T:TRP258
|
4.6
|
8.6
|
1.0
|
|
O
|
T:HOH582
|
4.6
|
36.2
|
1.0
|
|
CG
|
T:TRP118
|
4.7
|
15.7
|
1.0
|
|
HE1
|
T:PHE257
|
4.8
|
9.2
|
1.0
|
|
CD1
|
T:PHE257
|
4.8
|
9.2
|
1.0
|
|
HB2
|
T:CYS120
|
4.8
|
7.8
|
1.0
|
|
CB
|
T:CYS120
|
4.9
|
7.8
|
1.0
|
|
HD1
|
T:TRP118
|
4.9
|
18.5
|
1.0
|
|
O
|
T:THR114
|
4.9
|
8.2
|
1.0
|
|
HE1
|
T:TRP258
|
4.9
|
8.4
|
1.0
|
|
O
|
T:HOH643
|
5.0
|
32.8
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 6g7r
Go back to
Chlorine Binding Sites List in 6g7r
Chlorine binding site 4 out
of 4 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 Chlorine with other atoms in the Cl 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
|
T:Cl406
b:30.1
occ:1.00
|
H
|
T:HIS13
|
2.0
|
8.9
|
1.0
|
|
HA
|
T:ILE12
|
2.7
|
8.7
|
1.0
|
|
O
|
T:HOH662
|
2.8
|
33.4
|
1.0
|
|
HB
|
T:ILE12
|
2.9
|
10.1
|
1.0
|
|
O
|
T:HOH578
|
2.9
|
15.1
|
1.0
|
|
N
|
T:HIS13
|
3.0
|
8.9
|
1.0
|
|
HZ3
|
T:LYS98
|
3.0
|
26.6
|
1.0
|
|
HE1
|
T:TYR44
|
3.1
|
12.0
|
1.0
|
|
OD2
|
T:ASP46
|
3.2
|
24.6
|
1.0
|
|
CA
|
T:ILE12
|
3.4
|
8.4
|
1.0
|
|
HD2
|
T:HIS13
|
3.4
|
12.7
|
1.0
|
|
HE2
|
T:LYS98
|
3.4
|
20.3
|
1.0
|
|
O
|
T:HOH511
|
3.4
|
37.2
|
1.0
|
|
HG21
|
T:ILE12
|
3.4
|
10.9
|
1.0
|
|
HB2
|
T:HIS13
|
3.5
|
11.6
|
1.0
|
|
CB
|
T:ILE12
|
3.5
|
9.8
|
1.0
|
|
C
|
T:ILE12
|
3.7
|
8.6
|
1.0
|
|
O
|
T:HIS13
|
3.7
|
10.8
|
1.0
|
|
HD3
|
T:LYS98
|
3.7
|
18.5
|
1.0
|
|
NZ
|
T:LYS98
|
3.7
|
27.8
|
1.0
|
|
CG
|
T:ASP46
|
3.8
|
18.6
|
1.0
|
|
HZ2
|
T:LYS98
|
3.9
|
25.7
|
1.0
|
|
CA
|
T:HIS13
|
3.9
|
10.1
|
1.0
|
|
CE
|
T:LYS98
|
4.0
|
20.2
|
1.0
|
|
HE1
|
T:PHE95
|
4.0
|
12.7
|
1.0
|
|
CG2
|
T:ILE12
|
4.0
|
11.1
|
1.0
|
|
HE1
|
M:HIS30
|
4.0
|
18.4
|
1.0
|
|
CE1
|
T:TYR44
|
4.1
|
12.7
|
1.0
|
|
CB
|
T:HIS13
|
4.1
|
11.8
|
1.0
|
|
HB2
|
T:ASP46
|
4.2
|
14.4
|
1.0
|
|
CD2
|
T:HIS13
|
4.2
|
12.3
|
1.0
|
|
C
|
T:HIS13
|
4.2
|
9.6
|
1.0
|
|
OD1
|
T:ASP46
|
4.3
|
19.8
|
1.0
|
|
HH
|
T:TYR44
|
4.3
|
17.1
|
0.0
|
|
CD
|
T:LYS98
|
4.4
|
18.8
|
1.0
|
|
HG22
|
T:ILE12
|
4.4
|
11.0
|
1.0
|
|
H
|
T:ASP46
|
4.4
|
11.9
|
1.0
|
|
HZ1
|
T:LYS98
|
4.5
|
26.8
|
1.0
|
|
O
|
T:TRP11
|
4.5
|
10.3
|
1.0
|
|
CG
|
T:HIS13
|
4.6
|
12.7
|
1.0
|
|
CB
|
T:ASP46
|
4.6
|
14.2
|
1.0
|
|
OH
|
T:TYR44
|
4.6
|
16.9
|
1.0
|
|
N
|
T:ILE12
|
4.7
|
8.3
|
1.0
|
|
HG
|
T:SER90
|
4.7
|
23.9
|
0.0
|
|
HG23
|
T:ILE12
|
4.8
|
10.9
|
1.0
|
|
HA
|
T:HIS13
|
4.8
|
10.3
|
1.0
|
|
CE1
|
T:PHE95
|
4.8
|
13.1
|
1.0
|
|
HD1
|
T:TYR44
|
4.8
|
11.6
|
1.0
|
|
HE3
|
T:LYS98
|
4.8
|
20.8
|
1.0
|
|
CZ
|
T:TYR44
|
4.9
|
13.2
|
1.0
|
|
CG1
|
T:ILE12
|
4.9
|
10.6
|
1.0
|
|
O
|
T:ILE12
|
4.9
|
9.8
|
1.0
|
|
HD1
|
T:PHE95
|
4.9
|
12.7
|
1.0
|
|
CE1
|
M:HIS30
|
4.9
|
21.0
|
1.0
|
|
HD2
|
T:LYS98
|
5.0
|
18.7
|
1.0
|
|
HB3
|
T:HIS13
|
5.0
|
11.8
|
1.0
|
|
CD1
|
T:TYR44
|
5.0
|
11.8
|
1.0
|
|
HG13
|
T:ILE12
|
5.0
|
10.8
|
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: Sat Jul 27 23:49:06 2024
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