Chlorine in PDB 6z7r: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1, PDB code: 6z7r 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) 58.05 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.125, 93.686, 98.433, 90.00, 93.26, 90.00
R / Rfree (%) 18.8 / 24.2

Other elements in 6z7r:

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Krypton (Kr) 42 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 Krypton Gas - Structure WTKR1 (pdb code 6z7r). 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 Krypton Gas - Structure WTKR1, PDB code: 6z7r:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6z7r

Go back to Chlorine Binding Sites List in 6z7r
Chlorine binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


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 Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:17.3
occ:1.00
HG1 B:THR80 2.2 22.6 1.0
HD22 B:ASN113 2.2 22.7 1.0
H B:ALA81 2.6 16.9 1.0
HE1 B:PHE110 2.7 24.8 1.0
HA B:CYS78 2.8 18.0 1.0
OG1 B:THR80 3.0 18.7 1.0
HB2 B:ALA81 3.0 13.6 1.0
ND2 B:ASN113 3.0 18.8 1.0
HB2 B:CYS78 3.0 11.9 1.0
HD2 B:PRO421 3.1 24.9 1.0
HG2 B:PRO421 3.1 16.5 1.0
HD3 B:PRO421 3.2 24.9 1.0
N B:ALA81 3.2 14.0 1.0
CD B:PRO421 3.4 20.6 1.0
HB3 B:ASN113 3.4 29.8 1.0
CA B:CYS78 3.4 14.9 1.0
HD21 B:ASN113 3.4 22.7 1.0
CE1 B:PHE110 3.6 20.5 1.0
H B:THR80 3.6 16.7 1.0
C B:CYS78 3.6 10.3 1.0
CG B:PRO421 3.6 13.7 1.0
O B:CYS78 3.7 12.8 1.0
CB B:CYS78 3.7 9.8 1.0
CB B:ALA81 3.7 11.2 1.0
HB3 B:ALA81 3.7 13.6 1.0
HD1 B:PHE110 3.8 29.2 1.0
HG3 B:PRO421 3.9 16.5 1.0
N B:THR80 4.0 13.8 1.0
CB B:THR80 4.0 14.8 1.0
C B:THR80 4.0 13.4 1.0
CA B:ALA81 4.0 12.5 1.0
CG B:ASN113 4.1 20.8 1.0
HB3 B:CYS78 4.1 11.9 1.0
CD1 B:PHE110 4.1 24.2 1.0
CB B:ASN113 4.2 24.7 1.0
CA B:THR80 4.2 13.3 1.0
HB B:THR80 4.2 17.9 1.0
HA B:ALA81 4.3 15.1 1.0
N B:PRO79 4.4 17.1 1.0
HD2 B:PRO79 4.4 19.2 1.0
HB1 B:ALA81 4.6 13.6 1.0
O B:VAL77 4.6 12.6 1.0
CZ B:PHE110 4.6 18.6 1.0
HB2 B:ASN113 4.6 29.8 1.0
HA B:ALA420 4.6 11.0 1.0
HZ B:PHE110 4.6 22.5 1.0
N B:CYS78 4.7 16.9 1.0
HB1 B:ALA420 4.8 19.4 1.0
C B:PRO79 4.8 10.9 1.0
N B:PRO421 4.9 17.5 1.0
HE1 B:MET183 4.9 25.8 1.0
CD B:PRO79 5.0 15.9 1.0

Chlorine binding site 2 out of 2 in 6z7r

Go back to Chlorine Binding Sites List in 6z7r
Chlorine binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


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 Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:16.0
occ:1.00
HG1 D:THR80 2.1 14.5 1.0
HD22 D:ASN113 2.4 17.2 1.0
HE1 D:PHE110 2.6 17.4 1.0
H D:ALA81 2.6 11.0 1.0
HA D:CYS78 2.8 7.2 1.0
OG1 D:THR80 3.0 11.9 1.0
HB2 D:ALA81 3.0 20.8 1.0
HD3 D:PRO421 3.0 24.0 1.0
HD2 D:PRO421 3.1 24.0 1.0
HB2 D:CYS78 3.2 6.8 1.0
N D:ALA81 3.2 9.0 1.0
ND2 D:ASN113 3.3 14.2 1.0
HG2 D:PRO421 3.3 20.2 1.0
CD D:PRO421 3.4 19.9 1.0
HB3 D:ASN113 3.4 18.5 1.0
CE1 D:PHE110 3.4 14.3 1.0
CA D:CYS78 3.5 6.0 1.0
H D:THR80 3.6 18.0 1.0
HD1 D:PHE110 3.6 20.5 1.0
C D:CYS78 3.7 7.6 1.0
HD21 D:ASN113 3.7 17.2 1.0
CB D:ALA81 3.7 17.2 1.0
CG D:PRO421 3.7 16.7 1.0
O D:CYS78 3.8 10.3 1.0
HB3 D:ALA81 3.8 20.8 1.0
CB D:CYS78 3.8 6.0 1.0
CB D:THR80 3.9 9.8 1.0
HG3 D:PRO421 3.9 20.2 1.0
CA D:ALA81 3.9 9.2 1.0
N D:THR80 3.9 14.9 1.0
HB D:THR80 4.0 12.0 1.0
CD1 D:PHE110 4.0 16.9 1.0
C D:THR80 4.0 9.3 1.0
CA D:THR80 4.1 12.1 1.0
HA D:ALA81 4.2 11.2 1.0
HB3 D:CYS78 4.2 6.8 1.0
CG D:ASN113 4.2 16.1 1.0
CB D:ASN113 4.2 15.3 1.0
N D:PRO79 4.4 11.7 1.0
HA D:ALA420 4.5 21.2 1.0
HB1 D:ALA81 4.5 20.8 1.0
CZ D:PHE110 4.5 17.4 1.0
HD2 D:PRO79 4.5 17.1 1.0
HZ D:PHE110 4.6 21.1 1.0
HB2 D:ASN113 4.7 18.5 1.0
O D:VAL77 4.7 14.5 1.0
N D:CYS78 4.7 11.3 1.0
C D:PRO79 4.8 13.4 1.0
N D:PRO421 4.8 17.8 1.0
HB1 D:ALA420 4.9 17.1 1.0
HE1 D:MET183 4.9 13.5 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 Dec 12 14:45:38 2020

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