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Chlorine in PDB 6z8o: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr

Enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o 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) 39.12 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.716, 97.022, 121.318, 90.00, 104.66, 90.00
R / Rfree (%) 22.6 / 27.5

Other elements in 6z8o:

The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Krypton (Kr) 20 atoms
Iron (Fe) 36 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr (pdb code 6z8o). 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 G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6z8o

Go back to Chlorine Binding Sites List in 6z8o
Chlorine binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr


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 Krypton Gas - Structure G491A-Kr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:29.4
occ:1.00
HD22 B:ASN113 2.3 42.3 1.0
HG1 B:THR80 2.4 27.8 1.0
HE1 B:PHE110 2.5 36.1 1.0
H B:ALA81 2.7 32.7 1.0
HA B:CYS78 2.8 45.3 1.0
HB2 B:ALA81 2.9 37.9 1.0
HD3 B:PRO421 3.0 46.2 1.0
ND2 B:ASN113 3.1 34.1 1.0
OG1 B:THR80 3.1 21.9 1.0
HB2 B:CYS78 3.1 39.2 1.0
HG2 B:PRO421 3.2 43.2 1.0
CE1 B:PHE110 3.3 28.9 1.0
HD2 B:PRO421 3.3 46.2 1.0
N B:ALA81 3.4 26.1 1.0
HB3 B:ASN113 3.4 45.5 1.0
CD B:PRO421 3.4 37.3 1.0
HG3 B:PRO421 3.4 43.2 1.0
HD21 B:ASN113 3.4 42.3 1.0
CA B:CYS78 3.5 36.5 1.0
CG B:PRO421 3.5 34.9 1.0
HD1 B:PHE110 3.5 44.6 1.0
CB B:ALA81 3.7 30.4 1.0
H B:THR80 3.7 27.9 1.0
CB B:CYS78 3.7 31.5 1.0
HB3 B:ALA81 3.7 37.9 1.0
CD1 B:PHE110 3.8 36.0 1.0
C B:CYS78 3.8 22.6 1.0
HB3 B:CYS78 3.9 39.2 1.0
CA B:ALA81 4.0 32.2 1.0
O B:CYS78 4.1 21.9 1.0
CG B:ASN113 4.1 37.0 1.0
N B:THR80 4.1 22.1 1.0
CB B:ASN113 4.2 36.8 1.0
C B:THR80 4.2 27.1 1.0
CB B:THR80 4.3 27.0 1.0
HA B:ALA81 4.3 40.1 1.0
CZ B:PHE110 4.4 28.2 1.0
CA B:THR80 4.4 27.5 1.0
HB1 B:ALA81 4.5 37.9 1.0
HZ B:PHE110 4.5 35.3 1.0
N B:PRO79 4.6 23.8 1.0
HD2 B:PRO79 4.6 28.4 1.0
HB B:THR80 4.6 33.8 1.0
HA B:ALA420 4.7 40.8 1.0
O B:VAL77 4.7 30.9 1.0
HB2 B:ASN113 4.7 45.5 1.0
N B:CYS78 4.8 26.4 1.0
HE1 B:MET183 4.8 31.7 1.0
N B:PRO421 4.8 32.6 1.0
HD1 B:TYR114 4.9 44.1 1.0
C B:ASN113 4.9 33.8 1.0
H B:TYR114 5.0 41.7 1.0
CB B:PRO421 5.0 33.6 1.0
HB1 B:ALA420 5.0 43.2 1.0

Chlorine binding site 2 out of 2 in 6z8o

Go back to Chlorine Binding Sites List in 6z8o
Chlorine binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr


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 Krypton Gas - Structure G491A-Kr within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:37.3
occ:1.00
HD22 D:ASN113 2.5 33.8 1.0
HE1 D:PHE110 2.6 50.4 1.0
HG1 D:THR80 2.6 42.7 1.0
HD3 D:PRO421 2.8 48.0 1.0
HA D:CYS78 2.8 38.5 1.0
H D:ALA81 2.9 38.4 1.0
HB2 D:CYS78 3.0 48.5 1.0
HD2 D:PRO421 3.0 48.0 1.0
HG2 D:PRO421 3.1 51.8 1.0
HB2 D:ALA81 3.1 40.2 1.0
ND2 D:ASN113 3.2 27.0 1.0
CD D:PRO421 3.2 38.8 1.0
OG1 D:THR80 3.3 34.4 1.0
HG3 D:PRO421 3.4 51.8 1.0
CG D:PRO421 3.4 42.0 1.0
HD21 D:ASN113 3.5 33.8 1.0
CE1 D:PHE110 3.5 40.8 1.0
CA D:CYS78 3.5 30.9 1.0
HB3 D:ASN113 3.5 51.5 1.0
CB D:CYS78 3.6 39.2 1.0
N D:ALA81 3.6 30.8 1.0
HB3 D:CYS78 3.8 48.5 1.0
CB D:ALA81 3.8 32.3 1.0
HB3 D:ALA81 3.9 40.2 1.0
H D:THR80 3.9 35.8 1.0
C D:CYS78 4.0 27.9 1.0
HD1 D:PHE110 4.1 54.3 1.0
CG D:ASN113 4.1 33.6 1.0
O D:CYS78 4.2 29.6 1.0
CD1 D:PHE110 4.2 44.0 1.0
CA D:ALA81 4.3 30.9 1.0
CB D:ASN113 4.3 41.7 1.0
HZ D:PHE110 4.3 42.5 1.0
CZ D:PHE110 4.4 34.2 1.0
HA D:ALA420 4.4 42.7 1.0
N D:THR80 4.4 28.7 1.0
C D:THR80 4.4 32.1 1.0
CB D:THR80 4.5 30.1 1.0
O D:VAL77 4.5 30.3 1.0
HA D:ALA81 4.5 38.5 1.0
HB1 D:ALA420 4.6 51.8 1.0
N D:PRO421 4.6 36.0 1.0
HD2 D:PRO79 4.6 30.2 1.0
HB1 D:ALA81 4.6 40.2 1.0
CA D:THR80 4.7 31.0 1.0
HB D:THR80 4.7 37.5 1.0
N D:PRO79 4.7 26.1 1.0
N D:CYS78 4.8 37.1 1.0
CB D:PRO421 4.8 43.3 1.0
HB2 D:SER117 4.9 51.1 1.0
HB2 D:ASN113 4.9 51.5 1.0
C D:ASN113 5.0 36.4 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: Sat Jul 12 22:18:29 2025

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