Chlorine in PDB 6z9g: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
Enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
All present enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2:
1.12.7.2;
Protein crystallography data
The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2, PDB code: 6z9g
was solved by
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
I.A.C.Pereira,
P.M.Matias,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.20 /
1.76
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.306,
93.815,
126.951,
90.00,
105.20,
90.00
|
R / Rfree (%)
|
19.2 /
24
|
Other elements in 6z9g:
The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
(pdb code 6z9g). 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 [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2, PDB code: 6z9g:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 6z9g
Go back to
Chlorine Binding Sites List in 6z9g
Chlorine binding site 1 out
of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl504
b:10.5
occ:1.00
|
HG1
|
B:THR80
|
2.1
|
16.5
|
1.0
|
HD22
|
B:ASN113
|
2.2
|
16.3
|
1.0
|
HE1
|
B:PHE110
|
2.5
|
21.1
|
1.0
|
H
|
B:ALA81
|
2.6
|
13.5
|
1.0
|
HA
|
B:CYS78
|
2.8
|
24.3
|
1.0
|
OG1
|
B:THR80
|
2.9
|
13.8
|
1.0
|
HB2
|
B:ALA81
|
2.9
|
13.4
|
1.0
|
ND2
|
B:ASN113
|
3.0
|
13.5
|
1.0
|
HB2
|
B:CYS78
|
3.1
|
18.6
|
1.0
|
HD3
|
B:PRO421
|
3.1
|
20.1
|
1.0
|
N
|
B:ALA81
|
3.2
|
11.2
|
1.0
|
HD2
|
B:PRO421
|
3.3
|
20.1
|
1.0
|
HG2
|
B:PRO421
|
3.3
|
26.5
|
1.0
|
HB3
|
B:ASN113
|
3.4
|
20.7
|
1.0
|
HD21
|
B:ASN113
|
3.4
|
16.3
|
1.0
|
CE1
|
B:PHE110
|
3.4
|
17.6
|
1.0
|
CA
|
B:CYS78
|
3.5
|
20.2
|
1.0
|
CD
|
B:PRO421
|
3.5
|
16.7
|
1.0
|
H
|
B:THR80
|
3.6
|
10.7
|
1.0
|
CB
|
B:ALA81
|
3.6
|
11.1
|
1.0
|
HB3
|
B:ALA81
|
3.6
|
13.4
|
1.0
|
C
|
B:CYS78
|
3.6
|
8.0
|
1.0
|
O
|
B:CYS78
|
3.7
|
10.4
|
1.0
|
HD1
|
B:PHE110
|
3.7
|
26.7
|
1.0
|
CB
|
B:CYS78
|
3.7
|
15.5
|
1.0
|
CG
|
B:PRO421
|
3.8
|
22.1
|
1.0
|
CA
|
B:ALA81
|
3.9
|
16.3
|
1.0
|
N
|
B:THR80
|
3.9
|
8.9
|
1.0
|
CB
|
B:THR80
|
4.0
|
8.2
|
1.0
|
HG3
|
B:PRO421
|
4.0
|
26.5
|
1.0
|
C
|
B:THR80
|
4.0
|
17.7
|
1.0
|
CD1
|
B:PHE110
|
4.0
|
22.2
|
1.0
|
CG
|
B:ASN113
|
4.0
|
12.9
|
1.0
|
HB3
|
B:CYS78
|
4.1
|
18.6
|
1.0
|
HB
|
B:THR80
|
4.1
|
9.9
|
1.0
|
CB
|
B:ASN113
|
4.1
|
17.2
|
1.0
|
CA
|
B:THR80
|
4.1
|
9.6
|
1.0
|
HA
|
B:ALA81
|
4.2
|
19.6
|
1.0
|
N
|
B:PRO79
|
4.4
|
12.0
|
1.0
|
HD2
|
B:PRO79
|
4.5
|
14.3
|
1.0
|
HB1
|
B:ALA81
|
4.5
|
13.4
|
1.0
|
CZ
|
B:PHE110
|
4.5
|
22.0
|
1.0
|
HZ
|
B:PHE110
|
4.6
|
26.4
|
1.0
|
HB2
|
B:ASN113
|
4.6
|
20.7
|
1.0
|
HA
|
B:ALA420
|
4.7
|
24.4
|
1.0
|
O
|
B:VAL77
|
4.7
|
9.3
|
1.0
|
HB1
|
B:ALA420
|
4.7
|
18.6
|
1.0
|
N
|
B:CYS78
|
4.8
|
14.5
|
1.0
|
C
|
B:PRO79
|
4.8
|
14.3
|
1.0
|
HE1
|
B:MET183
|
4.8
|
20.0
|
1.0
|
HD1
|
B:TYR114
|
4.9
|
27.0
|
1.0
|
N
|
B:PRO421
|
5.0
|
17.5
|
1.0
|
O
|
B:THR80
|
5.0
|
11.3
|
1.0
|
CD
|
B:PRO79
|
5.0
|
11.9
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 6z9g
Go back to
Chlorine Binding Sites List in 6z9g
Chlorine binding site 2 out
of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl504
b:11.3
occ:1.00
|
HG1
|
D:THR80
|
2.1
|
17.7
|
1.0
|
HD22
|
D:ASN113
|
2.3
|
17.3
|
1.0
|
H
|
D:ALA81
|
2.6
|
10.4
|
1.0
|
HE1
|
D:PHE110
|
2.7
|
18.2
|
1.0
|
HA
|
D:CYS78
|
2.7
|
20.5
|
1.0
|
OG1
|
D:THR80
|
2.9
|
14.7
|
1.0
|
HB2
|
D:ALA81
|
2.9
|
11.7
|
1.0
|
HB2
|
D:CYS78
|
3.0
|
15.7
|
1.0
|
HD3
|
D:PRO421
|
3.0
|
17.3
|
1.0
|
ND2
|
D:ASN113
|
3.0
|
14.4
|
1.0
|
HD2
|
D:PRO421
|
3.2
|
17.3
|
1.0
|
HG2
|
D:PRO421
|
3.2
|
24.6
|
1.0
|
N
|
D:ALA81
|
3.2
|
8.6
|
1.0
|
HD21
|
D:ASN113
|
3.3
|
17.3
|
1.0
|
CD
|
D:PRO421
|
3.4
|
14.4
|
1.0
|
CA
|
D:CYS78
|
3.4
|
17.1
|
1.0
|
HB3
|
D:ASN113
|
3.6
|
14.2
|
1.0
|
CB
|
D:ALA81
|
3.6
|
9.8
|
1.0
|
C
|
D:CYS78
|
3.6
|
12.2
|
1.0
|
CE1
|
D:PHE110
|
3.6
|
15.1
|
1.0
|
H
|
D:THR80
|
3.6
|
9.6
|
1.0
|
CB
|
D:CYS78
|
3.6
|
13.1
|
1.0
|
HB3
|
D:ALA81
|
3.6
|
11.7
|
1.0
|
CG
|
D:PRO421
|
3.6
|
20.5
|
1.0
|
O
|
D:CYS78
|
3.6
|
11.7
|
1.0
|
HD1
|
D:PHE110
|
3.8
|
16.6
|
1.0
|
HG3
|
D:PRO421
|
3.8
|
24.6
|
1.0
|
CA
|
D:ALA81
|
3.9
|
8.9
|
1.0
|
N
|
D:THR80
|
4.0
|
8.0
|
1.0
|
CB
|
D:THR80
|
4.0
|
11.7
|
1.0
|
C
|
D:THR80
|
4.0
|
13.7
|
1.0
|
HB3
|
D:CYS78
|
4.0
|
15.7
|
1.0
|
CG
|
D:ASN113
|
4.1
|
13.5
|
1.0
|
CD1
|
D:PHE110
|
4.1
|
13.8
|
1.0
|
CA
|
D:THR80
|
4.2
|
8.4
|
1.0
|
HB
|
D:THR80
|
4.2
|
14.1
|
1.0
|
HA
|
D:ALA81
|
4.2
|
10.8
|
1.0
|
CB
|
D:ASN113
|
4.3
|
11.8
|
1.0
|
N
|
D:PRO79
|
4.3
|
10.3
|
1.0
|
HB1
|
D:ALA81
|
4.4
|
11.7
|
1.0
|
HD2
|
D:PRO79
|
4.5
|
10.0
|
1.0
|
HA
|
D:ALA420
|
4.5
|
10.9
|
1.0
|
O
|
D:VAL77
|
4.6
|
10.9
|
1.0
|
HB1
|
D:ALA420
|
4.6
|
15.6
|
1.0
|
CZ
|
D:PHE110
|
4.7
|
15.9
|
1.0
|
N
|
D:CYS78
|
4.7
|
10.1
|
1.0
|
HZ
|
D:PHE110
|
4.8
|
19.1
|
1.0
|
HB2
|
D:ASN113
|
4.8
|
14.2
|
1.0
|
C
|
D:PRO79
|
4.8
|
13.1
|
1.0
|
N
|
D:PRO421
|
4.8
|
22.4
|
1.0
|
HE1
|
D:MET183
|
4.9
|
11.7
|
1.0
|
HD1
|
D:TYR114
|
4.9
|
21.7
|
1.0
|
CD
|
D:PRO79
|
5.0
|
8.3
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 6z9g
Go back to
Chlorine Binding Sites List in 6z9g
Chlorine binding site 3 out
of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl504
b:15.3
occ:1.00
|
HD22
|
F:ASN113
|
2.1
|
14.6
|
1.0
|
HG1
|
F:THR80
|
2.3
|
18.7
|
1.0
|
HE1
|
F:PHE110
|
2.6
|
16.5
|
1.0
|
H
|
F:ALA81
|
2.7
|
14.0
|
1.0
|
HB2
|
F:ALA81
|
2.8
|
14.3
|
1.0
|
HA
|
F:CYS78
|
2.8
|
19.6
|
1.0
|
ND2
|
F:ASN113
|
2.9
|
12.1
|
1.0
|
OG1
|
F:THR80
|
3.0
|
15.6
|
1.0
|
HD3
|
F:PRO421
|
3.1
|
21.9
|
1.0
|
HB2
|
F:CYS78
|
3.1
|
16.3
|
1.0
|
HD2
|
F:PRO421
|
3.2
|
21.9
|
1.0
|
N
|
F:ALA81
|
3.3
|
11.6
|
1.0
|
HD21
|
F:ASN113
|
3.3
|
14.6
|
1.0
|
HG2
|
F:PRO421
|
3.3
|
16.1
|
1.0
|
CE1
|
F:PHE110
|
3.4
|
13.8
|
1.0
|
CD
|
F:PRO421
|
3.4
|
18.2
|
1.0
|
HB3
|
F:ASN113
|
3.4
|
12.8
|
1.0
|
CA
|
F:CYS78
|
3.5
|
16.3
|
1.0
|
CB
|
F:ALA81
|
3.6
|
11.9
|
1.0
|
C
|
F:CYS78
|
3.6
|
5.9
|
1.0
|
O
|
F:CYS78
|
3.6
|
6.0
|
1.0
|
H
|
F:THR80
|
3.7
|
19.1
|
1.0
|
HD1
|
F:PHE110
|
3.7
|
13.3
|
1.0
|
HB3
|
F:ALA81
|
3.7
|
14.3
|
1.0
|
CB
|
F:CYS78
|
3.7
|
13.5
|
1.0
|
CG
|
F:PRO421
|
3.8
|
13.4
|
1.0
|
CA
|
F:ALA81
|
3.9
|
18.1
|
1.0
|
HG3
|
F:PRO421
|
4.0
|
16.1
|
1.0
|
CD1
|
F:PHE110
|
4.0
|
11.1
|
1.0
|
N
|
F:THR80
|
4.0
|
15.9
|
1.0
|
CG
|
F:ASN113
|
4.0
|
10.9
|
1.0
|
C
|
F:THR80
|
4.1
|
16.4
|
1.0
|
CB
|
F:THR80
|
4.1
|
15.0
|
1.0
|
HB3
|
F:CYS78
|
4.1
|
16.3
|
1.0
|
HA
|
F:ALA81
|
4.2
|
21.8
|
1.0
|
CB
|
F:ASN113
|
4.2
|
10.7
|
1.0
|
CA
|
F:THR80
|
4.2
|
10.8
|
1.0
|
HB
|
F:THR80
|
4.3
|
18.1
|
1.0
|
N
|
F:PRO79
|
4.4
|
5.5
|
1.0
|
HB1
|
F:ALA81
|
4.4
|
14.3
|
1.0
|
HD2
|
F:PRO79
|
4.5
|
8.9
|
1.0
|
CZ
|
F:PHE110
|
4.5
|
17.1
|
1.0
|
HA
|
F:ALA420
|
4.5
|
15.6
|
1.0
|
HZ
|
F:PHE110
|
4.6
|
20.5
|
1.0
|
O
|
F:VAL77
|
4.7
|
9.3
|
1.0
|
HB2
|
F:ASN113
|
4.7
|
12.8
|
1.0
|
HB1
|
F:ALA420
|
4.7
|
14.3
|
1.0
|
N
|
F:CYS78
|
4.8
|
15.6
|
1.0
|
C
|
F:PRO79
|
4.8
|
8.3
|
1.0
|
HD1
|
F:TYR114
|
4.9
|
19.9
|
1.0
|
N
|
F:PRO421
|
4.9
|
19.1
|
1.0
|
HE1
|
F:MET183
|
4.9
|
14.8
|
1.0
|
CD
|
F:PRO79
|
5.0
|
7.4
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 6z9g
Go back to
Chlorine Binding Sites List in 6z9g
Chlorine binding site 4 out
of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl504
b:18.7
occ:1.00
|
HG1
|
H:THR80
|
2.3
|
33.5
|
1.0
|
HD22
|
H:ASN113
|
2.4
|
16.4
|
1.0
|
HE1
|
H:PHE110
|
2.7
|
27.9
|
1.0
|
H
|
H:ALA81
|
2.7
|
21.9
|
1.0
|
HA
|
H:CYS78
|
2.7
|
24.7
|
1.0
|
HB2
|
H:ALA81
|
2.9
|
22.7
|
1.0
|
OG1
|
H:THR80
|
3.0
|
27.9
|
1.0
|
HD3
|
H:PRO421
|
3.1
|
23.3
|
1.0
|
HB2
|
H:CYS78
|
3.1
|
22.5
|
1.0
|
ND2
|
H:ASN113
|
3.1
|
13.6
|
1.0
|
HG2
|
H:PRO421
|
3.2
|
20.2
|
1.0
|
HD2
|
H:PRO421
|
3.2
|
23.3
|
1.0
|
N
|
H:ALA81
|
3.3
|
18.2
|
1.0
|
CA
|
H:CYS78
|
3.4
|
20.5
|
1.0
|
CD
|
H:PRO421
|
3.4
|
19.4
|
1.0
|
HD21
|
H:ASN113
|
3.4
|
16.4
|
1.0
|
HB3
|
H:ASN113
|
3.5
|
31.9
|
1.0
|
CE1
|
H:PHE110
|
3.5
|
23.2
|
1.0
|
C
|
H:CYS78
|
3.6
|
17.3
|
1.0
|
CB
|
H:ALA81
|
3.6
|
18.9
|
1.0
|
CG
|
H:PRO421
|
3.6
|
16.8
|
1.0
|
H
|
H:THR80
|
3.7
|
19.6
|
1.0
|
CB
|
H:CYS78
|
3.7
|
18.7
|
1.0
|
HB3
|
H:ALA81
|
3.7
|
22.7
|
1.0
|
O
|
H:CYS78
|
3.8
|
15.8
|
1.0
|
HD1
|
H:PHE110
|
3.8
|
34.4
|
1.0
|
HG3
|
H:PRO421
|
3.8
|
20.2
|
1.0
|
CA
|
H:ALA81
|
4.0
|
20.8
|
1.0
|
N
|
H:THR80
|
4.0
|
16.4
|
1.0
|
HB3
|
H:CYS78
|
4.1
|
22.5
|
1.0
|
CD1
|
H:PHE110
|
4.1
|
28.6
|
1.0
|
CB
|
H:THR80
|
4.1
|
16.1
|
1.0
|
CG
|
H:ASN113
|
4.1
|
21.9
|
1.0
|
C
|
H:THR80
|
4.1
|
15.7
|
1.0
|
CB
|
H:ASN113
|
4.2
|
26.6
|
1.0
|
HA
|
H:ALA81
|
4.3
|
25.0
|
1.0
|
HB
|
H:THR80
|
4.3
|
19.4
|
1.0
|
CA
|
H:THR80
|
4.3
|
10.7
|
1.0
|
N
|
H:PRO79
|
4.3
|
10.8
|
1.0
|
HD2
|
H:PRO79
|
4.3
|
18.1
|
1.0
|
HB1
|
H:ALA81
|
4.4
|
22.7
|
1.0
|
O
|
H:VAL77
|
4.6
|
19.3
|
1.0
|
HA
|
H:ALA420
|
4.6
|
16.2
|
1.0
|
CZ
|
H:PHE110
|
4.6
|
25.0
|
1.0
|
N
|
H:CYS78
|
4.7
|
19.0
|
1.0
|
HZ
|
H:PHE110
|
4.7
|
30.1
|
1.0
|
HB1
|
H:ALA420
|
4.7
|
27.2
|
1.0
|
HB2
|
H:ASN113
|
4.7
|
31.9
|
1.0
|
C
|
H:PRO79
|
4.8
|
12.8
|
1.0
|
HE1
|
H:MET183
|
4.8
|
19.9
|
1.0
|
N
|
H:PRO421
|
4.9
|
20.6
|
1.0
|
CD
|
H:PRO79
|
4.9
|
15.0
|
1.0
|
HD1
|
H:TYR114
|
5.0
|
22.6
|
1.0
|
|
Reference:
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
I.A.C.Pereira,
P.M.Matias.
Exploring the Gas Access Routes in A [Nifese] Hydrogenase Using Crystals Pressurized with Krypton and Oxygen. J.Biol.Inorg.Chem. V. 25 863 2020.
ISSN: ESSN 1432-1327
PubMed: 32865640
DOI: 10.1007/S00775-020-01814-Y
Page generated: Mon Jul 29 18:00:46 2024
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