Iron in PDB 8ap2: 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;

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

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
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 40 binding sites of Iron where determined in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom, PDB code: 8ap2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 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 Iron with other atoms in the Fe 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:Fe601 b:16.5 occ:1.00 FE1 A:402601 0.0 16.5 1.0 C3 A:402601 1.7 12.0 1.0 C4 A:402601 1.9 14.6 1.0 C5 A:402601 1.9 16.2 1.0 S2 A:402601 2.3 15.6 1.0 S1 A:402601 2.3 17.1 1.0 SG A:CYS503 2.4 15.5 1.0 FE2 A:402601 2.6 16.8 1.0 O3 A:402601 2.9 14.7 1.0 O5 A:402601 2.9 17.0 1.0 N4 A:402601 3.0 13.5 1.0 CB A:CYS503 3.4 13.0 1.0 C1 A:402601 3.4 17.6 1.0 C2 A:402601 3.5 13.8 1.0 C7 A:402601 3.7 16.8 1.0 C6 A:402601 3.8 15.6 1.0 N1 A:402601 3.8 17.4 1.0 FE4 A:SF4602 4.1 14.9 1.0 C A:CYN607 4.1 16.5 1.0 S2 A:SF4602 4.3 14.6 1.0 CG A:PRO354 4.7 14.3 1.0 CE A:LYS358 4.7 15.6 1.0 O7 A:402601 4.7 18.1 1.0 N6 A:402601 4.8 16.2 1.0 CA A:CYS503 4.8 13.6 1.0 CD A:PRO354 5.0 15.0 1.0

Iron binding site 2 out of 40 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 Iron with other atoms in the Fe 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 A:Fe601 b:16.8 occ:1.00 FE2 A:402601 0.0 16.8 1.0 C7 A:402601 1.7 16.8 1.0 C A:CYN607 1.9 16.5 1.0 C6 A:402601 1.9 15.6 1.0 C5 A:402601 2.0 16.2 1.0 S2 A:402601 2.3 15.6 1.0 S1 A:402601 2.3 17.1 1.0 FE1 A:402601 2.6 16.5 1.0 O7 A:402601 2.9 18.1 1.0 O5 A:402601 2.9 17.0 1.0 N A:CYN607 3.0 17.9 1.0 N6 A:402601 3.1 16.2 1.0 C1 A:402601 3.4 17.6 1.0 N1 A:402601 3.4 17.4 1.0 C2 A:402601 3.5 13.8 1.0 C3 A:402601 3.8 12.0 1.0 C4 A:402601 3.8 14.6 1.0 CG A:PRO324 4.2 16.0 1.0 CD2 A:PHE417 4.3 17.4 1.0 CD A:PRO324 4.3 16.2 1.0 CB A:PRO324 4.5 15.1 1.0 SG A:CYS503 4.6 15.5 1.0 CE A:LYS358 4.7 15.6 1.0 N4 A:402601 4.7 13.5 1.0 O3 A:402601 4.8 14.7 1.0 NZ A:LYS358 4.8 14.1 1.0 CD A:PRO231 4.8 13.7 1.0 O A:CYS299 4.9 16.6 1.0 CG A:PRO231 4.9 15.8 1.0 CB A:PHE417 5.0 15.4 1.0

Iron binding site 3 out of 40 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 Iron with other atoms in the Fe 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 A:Fe602 b:14.8 occ:1.00 FE1 A:SF4602 0.0 14.8 1.0 S2 A:SF4602 2.2 14.6 1.0 S3 A:SF4602 2.2 14.3 1.0 S4 A:SF4602 2.3 13.8 1.0 SG A:CYS355 2.3 15.5 1.0 FE2 A:SF4602 2.6 14.9 1.0 FE4 A:SF4602 2.7 14.9 1.0 FE3 A:SF4602 2.7 14.8 1.0 CB A:CYS355 3.3 15.7 1.0 OG A:SER357 3.6 15.5 0.1 S1 A:SF4602 3.8 14.5 1.0 O A:HOH780 3.8 15.2 1.0 O3 A:402601 4.1 14.7 1.0 CA A:CYS355 4.3 15.9 1.0 C3 A:402601 4.6 12.0 1.0 CB A:SER357 4.6 14.4 0.9 CD A:PRO301 4.6 15.2 1.0 SG A:CYS499 4.7 14.9 1.0 SG A:CYS503 4.7 15.5 1.0 CG A:PRO301 4.7 17.2 1.0 SG A:CYS300 4.8 15.0 1.0 CB A:SER357 4.8 15.5 0.1 CG A:LYS358 4.9 15.7 1.0

Iron binding site 4 out of 40 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 Iron with other atoms in the Fe binding site number 4 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:Fe602 b:14.9 occ:1.00 FE2 A:SF4602 0.0 14.9 1.0 S4 A:SF4602 2.3 13.8 1.0 S1 A:SF4602 2.3 14.5 1.0 SG A:CYS499 2.3 14.9 1.0 S3 A:SF4602 2.3 14.3 1.0 FE1 A:SF4602 2.6 14.8 1.0 FE3 A:SF4602 2.7 14.8 1.0 FE4 A:SF4602 2.8 14.9 1.0 CB A:CYS499 3.2 14.3 1.0 N A:CYS499 3.8 15.4 1.0 S2 A:SF4602 3.8 14.6 1.0 CA A:CYS499 4.1 14.4 1.0 O A:HOH780 4.2 15.2 1.0 CA A:GLY506 4.3 14.9 1.0 SG A:CYS355 4.6 15.5 1.0 CB A:ALA498 4.6 17.5 1.0 C A:ALA498 4.6 14.4 1.0 SG A:CYS300 4.7 15.0 1.0 CA A:CYS503 4.8 13.6 1.0 N A:ALA498 4.8 14.0 1.0 CA A:ALA498 4.9 15.6 1.0 SG A:CYS503 5.0 15.5 1.0

Iron binding site 5 out of 40 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 Iron with other atoms in the Fe binding site number 5 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:Fe602 b:14.8 occ:1.00 FE3 A:SF4602 0.0 14.8 1.0 S4 A:SF4602 2.2 13.8 1.0 SG A:CYS300 2.3 15.0 1.0 S2 A:SF4602 2.3 14.6 1.0 S1 A:SF4602 2.3 14.5 1.0 FE1 A:SF4602 2.7 14.8 1.0 FE2 A:SF4602 2.7 14.9 1.0 FE4 A:SF4602 2.8 14.9 1.0 CB A:CYS300 3.4 14.7 1.0 S3 A:SF4602 3.9 14.3 1.0 CA A:CYS300 3.9 14.3 1.0 N A:ALA498 4.0 14.0 1.0 CB A:ALA498 4.1 17.5 1.0 N A:GLY302 4.3 12.8 1.0 C A:CYS300 4.3 15.3 1.0 CD A:PRO301 4.4 15.2 1.0 N A:PRO301 4.4 15.2 1.0 CA A:ALA498 4.6 15.6 1.0 N A:CYS499 4.7 15.4 1.0 OG A:SER357 4.7 15.5 0.1 SG A:CYS499 4.7 14.9 1.0 C2 A:402601 4.7 13.8 1.0 SG A:CYS503 4.8 15.5 1.0 SG A:CYS355 4.8 15.5 1.0 CA A:GLY302 4.8 13.4 1.0 SD A:MET497 4.9 17.2 1.0 C A:MET497 5.0 14.6 1.0

Iron binding site 6 out of 40 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 Iron with other atoms in the Fe binding site number 6 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:Fe602 b:14.9 occ:1.00 FE4 A:SF4602 0.0 14.9 1.0 S3 A:SF4602 2.2 14.3 1.0 S2 A:SF4602 2.3 14.6 1.0 S1 A:SF4602 2.3 14.5 1.0 SG A:CYS503 2.3 15.5 1.0 FE1 A:SF4602 2.7 14.8 1.0 FE2 A:SF4602 2.8 14.9 1.0 FE3 A:SF4602 2.8 14.8 1.0 CB A:CYS503 3.3 13.0 1.0 CA A:CYS503 3.4 13.6 1.0 C3 A:402601 3.8 12.0 1.0 S4 A:SF4602 3.9 13.8 1.0 N A:CYS503 3.9 15.3 1.0 O3 A:402601 4.0 14.7 1.0 FE1 A:402601 4.1 16.5 1.0 C2 A:402601 4.2 13.8 1.0 S2 A:402601 4.3 15.6 1.0 C A:GLY502 4.7 15.6 1.0 SG A:CYS355 4.7 15.5 1.0 C A:CYS503 4.8 14.5 1.0 SD A:MET497 4.8 17.2 1.0 SG A:CYS300 4.8 15.0 1.0 SG A:CYS499 4.9 14.9 1.0 CB A:CYS355 4.9 15.7 1.0

Iron binding site 7 out of 40 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 Iron with other atoms in the Fe binding site number 7 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:Fe603 b:15.4 occ:1.00 FE1 A:SF4603 0.0 15.4 1.0 S4 A:SF4603 2.3 14.4 1.0 SG A:CYS193 2.3 14.8 1.0 S2 A:SF4603 2.4 15.4 1.0 S3 A:SF4603 2.4 15.1 1.0 FE2 A:SF4603 2.8 15.0 1.0 FE3 A:SF4603 2.8 15.2 1.0 FE4 A:SF4603 2.8 15.1 1.0 N A:CYS193 3.6 14.6 1.0 CB A:CYS193 3.7 14.5 1.0 N A:GLY194 3.8 13.0 1.0 CG2 A:THR161 3.9 15.5 1.0 S1 A:SF4603 4.0 15.2 1.0 CA A:CYS193 4.0 13.2 1.0 N A:GLN195 4.1 13.3 1.0 C A:CYS193 4.2 13.6 1.0 N A:LEU192 4.4 14.5 1.0 C A:LEU192 4.7 16.4 1.0 SG A:CYS190 4.7 14.4 1.0 CA A:GLY194 4.7 12.3 1.0 SG A:CYS196 4.7 14.7 1.0 CB A:LEU191 4.7 14.0 1.0 N A:LEU191 4.7 13.2 1.0 CB A:GLN195 4.8 14.6 1.0 SG A:CYS157 4.8 14.9 1.0 CA A:LEU192 4.9 15.2 1.0 C A:GLY194 4.9 13.3 1.0 N A:CYS196 4.9 15.0 1.0

Iron binding site 8 out of 40 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 Iron with other atoms in the Fe binding site number 8 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:Fe603 b:15.0 occ:1.00 FE2 A:SF4603 0.0 15.0 1.0 S3 A:SF4603 2.2 15.1 1.0 S1 A:SF4603 2.3 15.2 1.0 SG A:CYS157 2.3 14.9 1.0 S4 A:SF4603 2.4 14.4 1.0 FE4 A:SF4603 2.7 15.1 1.0 FE3 A:SF4603 2.8 15.2 1.0 FE1 A:SF4603 2.8 15.4 1.0 CB A:CYS157 3.2 14.1 1.0 S2 A:SF4603 3.9 15.4 1.0 CA A:CYS157 4.0 13.7 1.0 OG1 A:THR163 4.1 17.2 1.0 CB A:ALA165 4.1 13.3 1.0 OG1 A:THR161 4.2 15.7 1.0 N A:MET166 4.3 15.5 1.0 CG2 A:THR161 4.4 15.5 1.0 N A:ALA165 4.6 14.8 1.0 CB A:MET166 4.7 13.6 1.0 CA A:ALA165 4.8 12.4 1.0 C A:ALA165 4.8 14.3 1.0 SG A:CYS196 4.8 14.7 1.0 C A:CYS157 4.8 14.6 1.0 SG A:CYS193 4.8 14.8 1.0 SG A:CYS190 4.8 14.4 1.0 O A:CYS157 4.9 15.8 1.0 CB A:THR161 5.0 14.6 1.0

Iron binding site 9 out of 40 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 Iron with other atoms in the Fe binding site number 9 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:Fe603 b:15.2 occ:1.00 FE3 A:SF4603 0.0 15.2 1.0 SG A:CYS196 2.3 14.7 1.0 S2 A:SF4603 2.3 15.4 1.0 S4 A:SF4603 2.3 14.4 1.0 S1 A:SF4603 2.4 15.2 1.0 FE2 A:SF4603 2.8 15.0 1.0 FE4 A:SF4603 2.8 15.1 1.0 FE1 A:SF4603 2.8 15.4 1.0 CB A:CYS196 3.3 15.0 1.0 N A:CYS196 3.8 15.0 1.0 S3 A:SF4603 3.9 15.1 1.0 CA A:CYS196 4.2 14.9 1.0 N A:GLY194 4.4 13.0 1.0 N A:GLN195 4.4 13.3 1.0 CA A:GLY194 4.5 12.3 1.0 CE A:MET166 4.5 17.6 1.0 CD1 A:LEU140 4.5 20.9 1.0 SG A:CYS190 4.7 14.4 1.0 SG A:CYS193 4.7 14.8 1.0 C A:GLY194 4.7 13.3 1.0 SG A:CYS157 4.8 14.9 1.0 CB A:CYS157 4.8 14.1 1.0 C A:GLN195 4.9 14.8 1.0

Iron binding site 10 out of 40 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 Iron with other atoms in the Fe binding site number 10 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:Fe603 b:15.1 occ:1.00 FE4 A:SF4603 0.0 15.1 1.0 S1 A:SF4603 2.2 15.2 1.0 SG A:CYS190 2.3 14.4 1.0 S3 A:SF4603 2.3 15.1 1.0 S2 A:SF4603 2.3 15.4 1.0 FE2 A:SF4603 2.7 15.0 1.0 FE3 A:SF4603 2.8 15.2 1.0 FE1 A:SF4603 2.8 15.4 1.0 CB A:CYS190 3.4 14.1 1.0 CA A:CYS190 3.8 13.7 1.0 N A:LEU191 3.9 13.2 1.0 S4 A:SF4603 3.9 14.4 1.0 N A:LEU192 4.0 14.5 1.0 CB A:ALA165 4.1 13.3 1.0 C A:CYS190 4.2 13.7 1.0 CA A:LEU192 4.6 15.2 1.0 CD2 A:PHE185 4.6 18.9 1.0 CD1 A:LEU140 4.6 20.9 1.0 SG A:CYS157 4.8 14.9 1.0 N A:CYS193 4.8 14.6 1.0 SG A:CYS196 4.8 14.7 1.0 CA A:LEU191 4.9 14.5 1.0 C A:LEU191 4.9 13.3 1.0

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