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Chlorine in PDB 8ap2: Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom

Enzymatic activity of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom

All present enzymatic activity of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom:
1.12.7.2;

Protein crystallography data

The structure of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom, PDB code: 8ap2 was solved by J.Duan, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.13 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.07, 71.5, 102.78, 90, 100.75, 90
R / Rfree (%) 15.9 / 19.1

Other elements in 8ap2:

The structure of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Iron (Fe) 40 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom (pdb code 8ap2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom, PDB code: 8ap2:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8ap2

Go back to Chlorine Binding Sites List in 8ap2
Chlorine binding site 1 out of 3 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:30.0
occ:1.00
 O A:HOH1173 3.1 33.6 1.0
O A:HOH1275 3.2 41.0 1.0
N A:ALA406 3.4 20.9 1.0
CD A:PRO405 3.5 25.3 1.0
CB A:ALA406 3.5 21.6 1.0
N A:PRO405 3.7 24.1 1.0
CB A:ASP404 3.7 23.3 1.0
C A:ASP404 3.9 22.8 1.0
CE A:LYS264 4.0 30.4 1.0
CE1 A:PHE266 4.0 18.3 1.0
NZ A:LYS264 4.1 31.7 1.0
CA A:ALA406 4.1 20.5 1.0
O A:HOH1341 4.1 53.0 1.0
CA A:ASP404 4.1 21.7 1.0
CG A:PRO405 4.2 26.3 1.0
C A:PRO405 4.4 22.2 1.0
CZ A:PHE266 4.5 19.0 1.0
O A:ASP404 4.5 21.3 1.0
CA A:PRO405 4.5 23.9 1.0
O A:HOH1183 4.7 48.3 1.0
CG A:ASP404 4.8 25.8 1.0

Chlorine binding site 2 out of 3 in 8ap2

Go back to Chlorine Binding Sites List in 8ap2
Chlorine binding site 2 out of 3 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl610

b:24.5
occ:1.00
 O B:HOH1236 2.9 41.5 1.0
O B:HOH1166 3.0 30.3 1.0
N B:ALA406 3.4 17.0 1.0
CD B:PRO405 3.5 22.2 1.0
CB B:ALA406 3.5 18.2 1.0
N B:PRO405 3.6 20.2 1.0
CB B:ASP404 3.6 19.5 1.0
CE B:LYS264 3.9 29.5 1.0
C B:ASP404 3.9 19.1 1.0
CG B:PRO405 4.0 22.6 1.0
NZ B:LYS264 4.0 32.3 1.0
CE1 B:PHE266 4.0 16.2 1.0
CA B:ALA406 4.1 15.9 1.0
CA B:ASP404 4.1 19.6 1.0
C B:PRO405 4.4 18.6 1.0
CZ B:PHE266 4.5 16.0 1.0
CA B:PRO405 4.5 20.6 1.0
O B:ASP404 4.5 17.3 1.0
CG B:ASP404 4.7 22.0 1.0
CB B:PRO405 5.0 22.6 1.0
OD1 B:ASP404 5.0 24.8 1.0

Chlorine binding site 3 out of 3 in 8ap2

Go back to Chlorine Binding Sites List in 8ap2
Chlorine binding site 3 out of 3 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl611

b:28.7
occ:1.00
 O B:HOH974 2.8 46.2 1.0
O B:HOH949 2.8 41.6 1.0
N B:GLN366 3.2 20.4 1.0
O B:HOH1201 3.4 40.8 1.0
CB B:GLN366 3.6 26.8 1.0
N B:PRO365 3.6 18.9 1.0
CG B:GLN366 3.6 33.1 1.0
CD B:PRO365 3.6 20.7 1.0
CB B:ARG364 3.9 18.5 1.0
CA B:GLN366 4.0 21.6 1.0
CZ B:PHE570 4.0 21.3 1.0
CB B:PRO365 4.0 22.4 1.0
C B:ARG364 4.1 17.5 1.0
C B:PRO365 4.1 21.3 1.0
CA B:PRO365 4.1 21.6 1.0
CG B:PRO365 4.2 22.6 1.0
CA B:ARG364 4.4 17.6 1.0
CD B:ARG364 4.5 21.6 1.0
CG B:ARG364 4.5 19.9 1.0
O B:HOH729 4.5 48.7 1.0
CE2 B:PHE570 4.7 20.5 1.0
O B:ARG364 4.7 17.5 1.0
C B:GLN366 4.8 19.2 1.0
O B:HOH1179 4.8 47.9 1.0
O B:HOH1260 4.8 33.6 1.0
CE1 B:PHE570 4.9 21.6 1.0
N B:MET367 4.9 17.3 1.0
CD B:GLN366 4.9 38.9 1.0

Reference:

J.Duan, A.Hemschemeier, D.J.Burr, S.T.Stripp, E.Hofmann, T.Happe. Cyanide Binding to [Fefe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew.Chem.Int.Ed.Engl. 2022.
ISSN: ESSN 1521-3773
PubMed: 36464641
DOI: 10.1002/ANIE.202216903
Page generated: Tue Jul 30 06:45:08 2024

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