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Chlorine in PDB 6z8j: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2

Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2

All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j 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) 42.41 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.864, 93.988, 98.612, 90.00, 93.16, 90.00
R / Rfree (%) 14 / 16.4

Other elements in 6z8j:

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 36 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 (pdb code 6z8j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6z8j

Go back to Chlorine Binding Sites List in 6z8j
Chlorine binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2


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 From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:9.5
occ:1.00
HD22 B:ASN113 2.3 11.3 1.0
H B:ALA81 2.6 10.1 1.0
HE1 B:PHE110 2.8 12.2 1.0
HA B:CYS78 2.8 10.4 1.0
HB1 B:ALA81 2.9 11.6 1.0
OG1 B:THR80 3.0 9.6 1.0
HD3 B:PRO421 3.0 11.6 1.0
HB2 B:CYS78 3.0 11.6 1.0
ND2 B:ASN113 3.1 9.4 1.0
HD2 B:PRO421 3.2 11.6 1.0
N B:ALA81 3.2 8.4 1.0
HG2 B:PRO421 3.3 11.2 1.0
HG1 B:THR80 3.3 11.6 1.0
HB3 B:ASN113 3.4 11.2 1.0
CD B:PRO421 3.4 9.6 1.0
CA B:CYS78 3.4 8.6 1.0
HD21 B:ASN113 3.5 11.3 1.0
CE1 B:PHE110 3.6 10.2 1.0
H B:THR80 3.6 9.9 1.0
HD1 B:PHE110 3.6 11.7 1.0
C B:CYS78 3.6 8.5 1.0
O B:CYS78 3.6 9.2 1.0
CB B:ALA81 3.6 9.7 1.0
CB B:CYS78 3.7 9.7 1.0
HB3 B:ALA81 3.7 11.6 1.0
CG B:PRO421 3.7 9.4 1.0
HG3 B:PRO421 3.9 11.2 1.0
N B:THR80 3.9 8.3 1.0
CB B:THR80 4.0 9.2 1.0
CA B:ALA81 4.0 9.2 1.0
CD1 B:PHE110 4.0 9.8 1.0
C B:THR80 4.0 8.7 1.0
HB3 B:CYS78 4.0 11.6 1.0
CG B:ASN113 4.1 9.6 1.0
HB B:THR80 4.1 11.0 1.0
CB B:ASN113 4.1 9.3 1.0
CA B:THR80 4.1 8.6 1.0
HA B:ALA81 4.2 11.1 1.0
N B:PRO79 4.4 8.4 1.0
HB2 B:ALA81 4.5 11.6 1.0
HA B:ALA420 4.5 11.3 1.0
HD2 B:PRO79 4.6 10.0 1.0
HB2 B:ASN113 4.6 11.2 1.0
O B:VAL77 4.6 9.2 1.0
HB2 B:ALA420 4.6 11.5 1.0
CZ B:PHE110 4.7 10.5 1.0
N B:CYS78 4.7 9.4 1.0
C B:PRO79 4.8 9.1 1.0
HE2 B:MET183 4.8 11.7 1.0
N B:PRO421 4.8 9.5 1.0
HZ B:PHE110 4.9 12.6 1.0
HD1 B:TYR114 4.9 13.2 1.0

Chlorine binding site 2 out of 2 in 6z8j

Go back to Chlorine Binding Sites List in 6z8j
Chlorine binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2


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 From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:9.7
occ:1.00
HD22 D:ASN113 2.3 12.1 1.0
H D:ALA81 2.6 10.5 1.0
HE1 D:PHE110 2.8 12.5 1.0
HA D:CYS78 2.8 10.7 1.0
OG1 D:THR80 3.0 9.5 1.0
HB1 D:ALA81 3.0 11.4 1.0
HD3 D:PRO421 3.0 10.4 1.0
HB2 D:CYS78 3.0 10.8 1.0
ND2 D:ASN113 3.2 10.1 1.0
HD2 D:PRO421 3.2 10.4 1.0
HG1 D:THR80 3.2 11.4 1.0
N D:ALA81 3.2 8.7 1.0
HG2 D:PRO421 3.3 11.0 1.0
CD D:PRO421 3.4 8.6 1.0
HB3 D:ASN113 3.4 11.7 1.0
CA D:CYS78 3.4 8.9 1.0
H D:THR80 3.5 10.4 1.0
HD21 D:ASN113 3.5 12.1 1.0
C D:CYS78 3.6 8.1 1.0
CE1 D:PHE110 3.6 10.4 1.0
O D:CYS78 3.6 8.8 1.0
HB3 D:ALA81 3.6 11.4 1.0
CB D:ALA81 3.6 9.5 1.0
HD1 D:PHE110 3.7 11.7 1.0
CB D:CYS78 3.7 9.0 1.0
CG D:PRO421 3.7 9.2 1.0
N D:THR80 3.9 8.7 1.0
HG3 D:PRO421 3.9 11.0 1.0
CA D:ALA81 4.0 8.9 1.0
CB D:THR80 4.0 9.0 1.0
C D:THR80 4.0 8.3 1.0
CD1 D:PHE110 4.0 9.8 1.0
HB3 D:CYS78 4.1 10.8 1.0
HB D:THR80 4.1 10.8 1.0
CG D:ASN113 4.1 9.8 1.0
CA D:THR80 4.1 8.6 1.0
CB D:ASN113 4.2 9.8 1.0
HA D:ALA81 4.2 10.7 1.0
N D:PRO79 4.3 7.8 1.0
HB2 D:ALA81 4.5 11.4 1.0
HA D:ALA420 4.5 11.5 1.0
HD2 D:PRO79 4.6 10.0 1.0
O D:VAL77 4.6 9.3 1.0
HB2 D:ASN113 4.6 11.7 1.0
HB2 D:ALA420 4.6 11.7 1.0
C D:PRO79 4.7 8.2 1.0
CZ D:PHE110 4.7 10.4 1.0
N D:CYS78 4.7 8.8 1.0
HE2 D:MET183 4.8 11.3 1.0
N D:PRO421 4.8 9.0 1.0
HZ D:PHE110 4.9 12.4 1.0
HD1 D:TYR114 4.9 11.9 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 17:58:23 2024

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