Chlorine in PDB 9er7: Hydrogenase-1 Ni-Sco State
Enzymatic activity of Hydrogenase-1 Ni-Sco State
All present enzymatic activity of Hydrogenase-1 Ni-Sco State:
1.12.99.6;
Protein crystallography data
The structure of Hydrogenase-1 Ni-Sco State, PDB code: 9er7
was solved by
S.B.Carr,
W.Li,
K.L.Wong,
P.A.Ash,
K.A.Vincent,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
66.20 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.79,
96.01,
182.79,
90,
90,
90
|
R / Rfree (%)
|
16.9 /
18.9
|
Other elements in 9er7:
The structure of Hydrogenase-1 Ni-Sco State also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Hydrogenase-1 Ni-Sco State
(pdb code 9er7). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Hydrogenase-1 Ni-Sco State, PDB code: 9er7:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 9er7
Go back to
Chlorine Binding Sites List in 9er7
Chlorine binding site 1 out
of 4 in the Hydrogenase-1 Ni-Sco State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Cl404
b:21.4
occ:1.00
|
O
|
S:HOH618
|
2.9
|
18.3
|
1.0
|
N
|
S:GLY256
|
3.1
|
16.4
|
1.0
|
N
|
S:CYS120
|
3.2
|
15.4
|
1.0
|
O
|
S:HOH667
|
3.2
|
28.0
|
1.0
|
CB
|
S:TRP118
|
3.7
|
17.0
|
1.0
|
CA
|
S:CYS120
|
3.7
|
14.2
|
1.0
|
CA
|
S:GLY256
|
3.8
|
16.4
|
1.0
|
CG2
|
S:THR114
|
3.8
|
16.0
|
1.0
|
N
|
S:GLY119
|
4.0
|
16.5
|
1.0
|
C
|
S:TRP118
|
4.1
|
17.8
|
1.0
|
C
|
S:GLY119
|
4.1
|
15.7
|
1.0
|
OD1
|
S:ASN255
|
4.2
|
19.6
|
1.0
|
C
|
S:ASN255
|
4.2
|
16.9
|
1.0
|
O
|
S:CYS120
|
4.3
|
14.0
|
1.0
|
CA
|
S:GLY119
|
4.3
|
15.5
|
1.0
|
CA
|
S:ASN255
|
4.3
|
16.1
|
1.0
|
O
|
S:TRP118
|
4.3
|
18.2
|
1.0
|
N
|
S:PHE257
|
4.4
|
16.2
|
1.0
|
O
|
S:GLU254
|
4.4
|
15.9
|
1.0
|
C
|
S:CYS120
|
4.4
|
13.9
|
1.0
|
C
|
S:GLY256
|
4.5
|
16.1
|
1.0
|
CA
|
S:TRP118
|
4.6
|
16.2
|
1.0
|
CD1
|
S:TRP258
|
4.6
|
15.4
|
1.0
|
O
|
S:HOH571
|
4.6
|
31.2
|
1.0
|
CG
|
S:TRP118
|
4.7
|
19.7
|
1.0
|
O
|
S:THR114
|
4.9
|
14.0
|
1.0
|
CD1
|
S:PHE257
|
4.9
|
15.2
|
1.0
|
CB
|
S:CYS120
|
4.9
|
14.3
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 9er7
Go back to
Chlorine Binding Sites List in 9er7
Chlorine binding site 2 out
of 4 in the Hydrogenase-1 Ni-Sco State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Cl405
b:21.1
occ:1.00
|
O
|
S:HOH579
|
3.1
|
22.6
|
1.0
|
O
|
S:HOH534
|
3.1
|
27.2
|
1.0
|
O
|
S:HOH520
|
3.2
|
25.3
|
1.0
|
N
|
S:HIS13
|
3.3
|
14.3
|
1.0
|
NZ
|
S:LYS98
|
3.3
|
24.1
|
1.0
|
CB
|
S:ILE12
|
3.5
|
15.6
|
1.0
|
CA
|
S:ILE12
|
3.5
|
13.4
|
1.0
|
OD2
|
S:ASP46
|
3.7
|
21.3
|
1.0
|
CE
|
S:LYS98
|
3.7
|
22.7
|
1.0
|
O
|
S:HIS13
|
3.9
|
14.2
|
1.0
|
CG2
|
S:ILE12
|
3.9
|
15.5
|
1.0
|
C
|
S:ILE12
|
3.9
|
13.7
|
1.0
|
O
|
S:HOH606
|
4.1
|
27.9
|
1.0
|
CD
|
S:LYS98
|
4.1
|
21.8
|
1.0
|
CE2
|
S:TYR44
|
4.1
|
18.9
|
1.0
|
CA
|
S:HIS13
|
4.2
|
13.9
|
1.0
|
CG
|
S:ASP46
|
4.2
|
21.5
|
1.0
|
CB
|
S:HIS13
|
4.4
|
14.3
|
1.0
|
C
|
S:HIS13
|
4.5
|
13.9
|
1.0
|
CE1
|
S:PHE95
|
4.5
|
16.5
|
1.0
|
OH
|
S:TYR44
|
4.5
|
20.6
|
1.0
|
CD2
|
S:HIS13
|
4.7
|
14.7
|
1.0
|
OD1
|
S:ASP46
|
4.7
|
23.5
|
1.0
|
CZ
|
S:TYR44
|
4.8
|
18.0
|
1.0
|
O
|
S:TRP11
|
4.8
|
14.8
|
1.0
|
N
|
S:ILE12
|
4.8
|
14.2
|
1.0
|
CG1
|
S:ILE12
|
4.8
|
16.0
|
1.0
|
CG
|
S:HIS13
|
4.9
|
14.2
|
1.0
|
CD1
|
S:PHE95
|
4.9
|
15.7
|
1.0
|
CB
|
S:ASP46
|
5.0
|
21.5
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 9er7
Go back to
Chlorine Binding Sites List in 9er7
Chlorine binding site 3 out
of 4 in the Hydrogenase-1 Ni-Sco State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cl404
b:21.8
occ:1.00
|
O
|
T:HOH604
|
3.0
|
18.6
|
1.0
|
N
|
T:GLY256
|
3.1
|
16.4
|
1.0
|
N
|
T:CYS120
|
3.1
|
16.5
|
1.0
|
O
|
T:HOH662
|
3.2
|
30.7
|
1.0
|
CB
|
T:TRP118
|
3.6
|
18.7
|
1.0
|
CA
|
T:CYS120
|
3.7
|
14.5
|
1.0
|
CG2
|
T:THR114
|
3.7
|
18.1
|
1.0
|
CA
|
T:GLY256
|
3.7
|
17.1
|
1.0
|
N
|
T:GLY119
|
4.0
|
17.2
|
1.0
|
C
|
T:TRP118
|
4.1
|
18.3
|
1.0
|
C
|
T:GLY119
|
4.1
|
16.9
|
1.0
|
C
|
T:ASN255
|
4.1
|
16.1
|
1.0
|
O
|
T:TRP118
|
4.2
|
18.8
|
1.0
|
OD1
|
T:ASN255
|
4.2
|
21.2
|
1.0
|
CA
|
T:GLY119
|
4.2
|
15.7
|
1.0
|
O
|
T:CYS120
|
4.3
|
16.0
|
1.0
|
CA
|
T:ASN255
|
4.3
|
16.7
|
1.0
|
N
|
T:PHE257
|
4.4
|
16.6
|
1.0
|
C
|
T:CYS120
|
4.4
|
15.8
|
1.0
|
O
|
T:GLU254
|
4.5
|
15.9
|
1.0
|
CA
|
T:TRP118
|
4.5
|
18.5
|
1.0
|
C
|
T:GLY256
|
4.5
|
16.4
|
1.0
|
CD1
|
T:TRP258
|
4.6
|
14.4
|
1.0
|
O
|
T:HOH616
|
4.6
|
30.9
|
1.0
|
CG
|
T:TRP118
|
4.7
|
21.4
|
1.0
|
O
|
T:THR114
|
4.8
|
15.7
|
1.0
|
CD1
|
T:PHE257
|
4.8
|
15.9
|
1.0
|
CB
|
T:CYS120
|
4.9
|
15.9
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 9er7
Go back to
Chlorine Binding Sites List in 9er7
Chlorine binding site 4 out
of 4 in the Hydrogenase-1 Ni-Sco State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cl405
b:21.0
occ:1.00
|
O
|
T:HOH607
|
3.1
|
24.1
|
1.0
|
O
|
T:HOH599
|
3.1
|
20.9
|
1.0
|
O
|
T:HOH554
|
3.2
|
25.8
|
1.0
|
NZ
|
T:LYS98
|
3.3
|
22.5
|
1.0
|
N
|
T:HIS13
|
3.3
|
14.9
|
1.0
|
CB
|
T:ILE12
|
3.5
|
16.9
|
1.0
|
CA
|
T:ILE12
|
3.6
|
14.8
|
1.0
|
CE
|
T:LYS98
|
3.7
|
20.2
|
1.0
|
OD2
|
T:ASP46
|
3.8
|
21.1
|
1.0
|
O
|
T:HIS13
|
3.9
|
17.0
|
1.0
|
CG2
|
T:ILE12
|
3.9
|
16.8
|
1.0
|
CD
|
T:LYS98
|
4.0
|
21.2
|
1.0
|
C
|
T:ILE12
|
4.0
|
16.2
|
1.0
|
CE2
|
T:TYR44
|
4.1
|
20.2
|
1.0
|
O
|
T:HOH618
|
4.1
|
24.9
|
1.0
|
CA
|
T:HIS13
|
4.3
|
15.8
|
1.0
|
CG
|
T:ASP46
|
4.3
|
21.6
|
1.0
|
CB
|
T:HIS13
|
4.4
|
17.1
|
1.0
|
CE1
|
T:PHE95
|
4.4
|
17.9
|
1.0
|
C
|
T:HIS13
|
4.5
|
16.6
|
1.0
|
OH
|
T:TYR44
|
4.6
|
19.5
|
1.0
|
CD2
|
T:HIS13
|
4.7
|
15.2
|
1.0
|
O
|
T:TRP11
|
4.8
|
16.8
|
1.0
|
OD1
|
T:ASP46
|
4.8
|
22.1
|
1.0
|
CD1
|
T:PHE95
|
4.9
|
17.0
|
1.0
|
CG1
|
T:ILE12
|
4.9
|
17.4
|
1.0
|
CZ
|
T:TYR44
|
4.9
|
19.9
|
1.0
|
N
|
T:ILE12
|
4.9
|
15.5
|
1.0
|
CG
|
T:HIS13
|
4.9
|
16.4
|
1.0
|
|
Reference:
S.B.Carr,
W.Li,
K.L.Wong,
R.M.Evans,
S.E.T.Kendall-Price,
P.A.Ash,
K.A.Vincent.
Glutamate Flick Enables Proton Tunnelling During Fast Redox Biocatalysis To Be Published.
Page generated: Sun Jul 13 16:35:14 2025
|