Iron in PDB 8pvm: Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

All present enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D:
1.12.7.2;

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm 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)	45.06 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.65, 69.83, 102.89, 90, 102.74, 90
R / Rfree (%)	14.3 / 17.5

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	6 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 Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D (pdb code 8pvm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm:
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 Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:14.2 occ:0.81 FE1 A:402601 0.0 14.2 0.8 C3 A:402601 1.7 12.3 0.8 C4 A:402601 1.9 12.8 0.8 C5 A:402601 1.9 15.2 0.8 S2 A:402601 2.3 15.6 0.8 S1 A:402601 2.3 15.1 0.8 SG A:CYS503 2.4 13.5 1.0 FE2 A:402601 2.6 16.4 0.8 O3 A:402601 2.9 15.0 0.8 O5 A:402601 3.0 15.5 0.8 N4 A:402601 3.1 11.1 0.8 CL A:CL615 3.2 25.3 0.2 CB A:CYS503 3.3 14.1 1.0 C1 A:402601 3.4 15.6 0.8 C2 A:402601 3.5 15.7 0.8 N1 A:402601 3.8 17.9 0.8 C7 A:402601 3.8 14.7 0.8 C6 A:402601 3.9 13.8 0.8 FE4 A:SF4602 4.1 13.9 1.0 S2 A:SF4602 4.3 13.9 1.0 CG A:PRO354 4.6 14.0 1.0 CA A:CYS503 4.8 14.2 1.0 CD A:PRO354 4.8 14.3 1.0 O7 A:402601 4.8 16.9 0.8 N6 A:402601 4.8 11.9 0.8 CE A:MET353 4.9 17.3 0.5 CE A:LYS358 4.9 14.3 1.0

Iron binding site 2 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:16.4 occ:0.81 FE2 A:402601 0.0 16.4 0.8 C7 A:402601 1.8 14.7 0.8 C6 A:402601 1.9 13.8 0.8 C5 A:402601 2.0 15.2 0.8 S2 A:402601 2.3 15.6 0.8 S1 A:402601 2.3 15.1 0.8 FE1 A:402601 2.6 14.2 0.8 O5 A:402601 2.8 15.5 0.8 O7 A:402601 2.9 16.9 0.8 N6 A:402601 3.1 11.9 0.8 N1 A:402601 3.3 17.9 0.8 C1 A:402601 3.4 15.6 0.8 C2 A:402601 3.5 15.7 0.8 C3 A:402601 3.7 12.3 0.8 C4 A:402601 3.7 12.8 0.8 CG A:PRO324 4.0 14.0 1.0 CB A:PRO324 4.3 13.6 1.0 CD A:PRO324 4.4 13.5 1.0 CD2 A:PHE417 4.4 15.8 1.0 SG A:CYS503 4.6 13.5 1.0 N4 A:402601 4.7 11.1 0.8 O3 A:402601 4.7 15.0 0.8 CD A:PRO231 4.7 14.8 1.0 CE A:LYS358 4.7 14.3 1.0 CL A:CL615 4.7 25.3 0.2 NZ A:LYS358 4.7 13.6 1.0 CE A:MET353 4.9 17.3 0.5 CG A:PRO231 4.9 17.4 1.0 CB A:PHE417 4.9 14.8 1.0

Iron binding site 3 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:14.7 occ:0.99 FE1 A:SF4602 0.0 14.7 1.0 SG A:CYS355 2.2 15.4 1.0 S2 A:SF4602 2.2 13.9 1.0 S4 A:SF4602 2.3 14.3 1.0 S3 A:SF4602 2.3 13.6 1.0 FE3 A:SF4602 2.7 13.6 1.0 FE4 A:SF4602 2.7 13.9 1.0 FE2 A:SF4602 2.7 14.2 1.0 CB A:CYS355 3.2 16.1 1.0 OG A:SER357 3.5 14.3 0.4 O A:HOH732 3.7 14.7 1.0 S1 A:SF4602 3.8 13.5 1.0 O3 A:402601 4.1 15.0 0.8 CA A:CYS355 4.3 16.1 1.0 CB A:SER357 4.6 14.2 0.6 C3 A:402601 4.6 12.3 0.8 CD A:PRO301 4.6 14.3 1.0 SG A:CYS503 4.7 13.5 1.0 SG A:CYS300 4.7 13.5 1.0 SG A:CYS499 4.7 13.8 1.0 CB A:SER357 4.7 13.8 0.4 CG A:PRO301 4.8 18.1 1.0 CG A:LYS358 4.8 13.0 1.0

Iron binding site 4 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:14.2 occ:0.99 FE2 A:SF4602 0.0 14.2 1.0 S1 A:SF4602 2.3 13.5 1.0 SG A:CYS499 2.3 13.8 1.0 S3 A:SF4602 2.3 13.6 1.0 S4 A:SF4602 2.3 14.3 1.0 FE1 A:SF4602 2.7 14.7 1.0 FE3 A:SF4602 2.7 13.6 1.0 FE4 A:SF4602 2.8 13.9 1.0 CB A:CYS499 3.2 14.2 1.0 N A:CYS499 3.9 12.2 1.0 S2 A:SF4602 3.9 13.9 1.0 O A:HOH732 4.0 14.7 1.0 CA A:CYS499 4.2 15.4 1.0 CA A:GLY506 4.3 14.5 1.0 SG A:CYS355 4.6 15.4 1.0 CB A:ALA498 4.7 14.2 1.0 C A:ALA498 4.7 12.4 1.0 SG A:CYS300 4.7 13.5 1.0 CA A:CYS503 4.8 14.2 1.0 N A:ALA498 4.9 13.3 1.0 SG A:CYS503 4.9 13.5 1.0

Iron binding site 5 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:13.6 occ:0.99 FE3 A:SF4602 0.0 13.6 1.0 SG A:CYS300 2.3 13.5 1.0 S2 A:SF4602 2.3 13.9 1.0 S4 A:SF4602 2.3 14.3 1.0 S1 A:SF4602 2.3 13.5 1.0 FE1 A:SF4602 2.7 14.7 1.0 FE2 A:SF4602 2.7 14.2 1.0 FE4 A:SF4602 2.7 13.9 1.0 CB A:CYS300 3.3 14.6 1.0 S3 A:SF4602 3.9 13.6 1.0 CA A:CYS300 3.9 13.3 1.0 N A:ALA498 4.0 13.3 1.0 CB A:ALA498 4.3 14.2 1.0 C A:CYS300 4.4 13.9 1.0 N A:GLY302 4.4 13.2 1.0 CD A:PRO301 4.5 14.3 1.0 N A:PRO301 4.5 13.9 1.0 OG A:SER357 4.6 14.3 0.4 SG A:CYS499 4.7 13.8 1.0 CA A:ALA498 4.7 13.4 1.0 C2 A:402601 4.7 15.7 0.8 SG A:CYS503 4.7 13.5 1.0 SD A:MET497 4.8 18.2 1.0 N A:CYS499 4.8 12.2 1.0 SG A:CYS355 4.8 15.4 1.0 CA A:GLY302 4.9 13.8 1.0

Iron binding site 6 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:13.9 occ:0.99 FE4 A:SF4602 0.0 13.9 1.0 S3 A:SF4602 2.3 13.6 1.0 SG A:CYS503 2.3 13.5 1.0 S1 A:SF4602 2.3 13.5 1.0 S2 A:SF4602 2.3 13.9 1.0 FE1 A:SF4602 2.7 14.7 1.0 FE3 A:SF4602 2.7 13.6 1.0 FE2 A:SF4602 2.8 14.2 1.0 CB A:CYS503 3.3 14.1 1.0 CA A:CYS503 3.5 14.2 1.0 C3 A:402601 3.9 12.3 0.8 S4 A:SF4602 3.9 14.3 1.0 N A:CYS503 3.9 13.3 1.0 O3 A:402601 4.0 15.0 0.8 FE1 A:402601 4.1 14.2 0.8 C2 A:402601 4.1 15.7 0.8 S2 A:402601 4.2 15.6 0.8 C A:GLY502 4.6 13.6 1.0 SD A:MET497 4.6 18.2 1.0 SG A:CYS355 4.7 15.4 1.0 SG A:CYS300 4.8 13.5 1.0 C A:CYS503 4.8 13.1 1.0 CB A:CYS355 4.9 16.1 1.0 SG A:CYS499 4.9 13.8 1.0

Iron binding site 7 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.2 occ:1.00 FE1 A:SF4603 0.0 14.2 1.0 S4 A:SF4603 2.3 14.0 1.0 SG A:CYS193 2.3 14.2 1.0 S2 A:SF4603 2.3 14.0 1.0 S3 A:SF4603 2.3 13.8 1.0 FE3 A:SF4603 2.8 13.8 1.0 FE2 A:SF4603 2.8 14.2 1.0 FE4 A:SF4603 2.8 13.9 1.0 N A:CYS193 3.6 13.4 1.0 CB A:CYS193 3.7 12.9 1.0 N A:GLY194 3.8 12.6 1.0 S1 A:SF4603 4.0 13.7 1.0 CG2 A:THR161 4.0 15.6 1.0 CA A:CYS193 4.1 12.6 1.0 N A:GLN195 4.2 13.1 1.0 C A:CYS193 4.2 13.5 1.0 N A:LEU192 4.4 14.2 1.0 C A:LEU192 4.6 14.1 1.0 CB A:LEU191 4.7 13.2 1.0 SG A:CYS196 4.7 14.7 1.0 CA A:GLY194 4.7 14.1 1.0 N A:LEU191 4.7 13.1 1.0 SG A:CYS190 4.7 13.8 1.0 CA A:LEU192 4.9 13.4 1.0 SG A:CYS157 4.9 13.5 1.0 CB A:GLN195 4.9 15.0 1.0 C A:GLY194 4.9 13.0 1.0 C A:LEU191 4.9 13.9 1.0 N A:CYS196 5.0 13.3 1.0

Iron binding site 8 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.2 occ:1.00 FE2 A:SF4603 0.0 14.2 1.0 S3 A:SF4603 2.3 13.8 1.0 S1 A:SF4603 2.3 13.7 1.0 S4 A:SF4603 2.3 14.0 1.0 SG A:CYS157 2.3 13.5 1.0 FE4 A:SF4603 2.7 13.9 1.0 FE3 A:SF4603 2.7 13.8 1.0 FE1 A:SF4603 2.8 14.2 1.0 CB A:CYS157 3.2 13.2 1.0 S2 A:SF4603 3.9 14.0 1.0 CA A:CYS157 3.9 12.7 1.0 OG1 A:THR163 4.1 15.6 1.0 OG1 A:THR161 4.1 13.7 1.0 CB A:ALA165 4.2 16.0 1.0 CG2 A:THR161 4.4 15.6 1.0 N A:MET166 4.5 13.9 1.0 N A:ALA165 4.7 14.2 1.0 CB A:MET166 4.7 15.3 1.0 C A:CYS157 4.8 13.7 1.0 SG A:CYS193 4.8 14.2 1.0 SG A:CYS196 4.8 14.7 1.0 CA A:ALA165 4.8 14.8 1.0 SG A:CYS190 4.9 13.8 1.0 O A:CYS157 4.9 14.4 1.0 CB A:THR161 4.9 13.4 1.0 C A:ALA165 4.9 15.6 1.0

Iron binding site 9 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:13.8 occ:1.00 FE3 A:SF4603 0.0 13.8 1.0 S2 A:SF4603 2.3 14.0 1.0 SG A:CYS196 2.3 14.7 1.0 S1 A:SF4603 2.3 13.7 1.0 S4 A:SF4603 2.3 14.0 1.0 FE2 A:SF4603 2.7 14.2 1.0 FE4 A:SF4603 2.8 13.9 1.0 FE1 A:SF4603 2.8 14.2 1.0 CB A:CYS196 3.3 14.4 1.0 N A:CYS196 3.9 13.3 1.0 S3 A:SF4603 3.9 13.8 1.0 CA A:CYS196 4.2 13.6 1.0 N A:GLY194 4.4 12.6 1.0 CE A:MET166 4.5 17.2 1.0 CD1 A:LEU140 4.5 22.5 1.0 N A:GLN195 4.5 13.1 1.0 CA A:GLY194 4.6 14.1 1.0 SG A:CYS190 4.7 13.8 1.0 SG A:CYS193 4.7 14.2 1.0 SG A:CYS157 4.7 13.5 1.0 C A:GLY194 4.8 13.0 1.0 CB A:CYS157 4.8 13.2 1.0 CB A:MET166 5.0 15.3 1.0

Iron binding site 10 out of 40 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:13.9 occ:1.00 FE4 A:SF4603 0.0 13.9 1.0 SG A:CYS190 2.3 13.8 1.0 S1 A:SF4603 2.3 13.7 1.0 S2 A:SF4603 2.3 14.0 1.0 S3 A:SF4603 2.3 13.8 1.0 FE2 A:SF4603 2.7 14.2 1.0 FE3 A:SF4603 2.8 13.8 1.0 FE1 A:SF4603 2.8 14.2 1.0 CB A:CYS190 3.4 14.2 1.0 CA A:CYS190 3.8 13.3 1.0 N A:LEU191 3.8 13.1 1.0 N A:LEU192 3.9 14.2 1.0 S4 A:SF4603 3.9 14.0 1.0 CB A:ALA165 4.1 16.0 1.0 C A:CYS190 4.2 14.4 1.0 CA A:LEU192 4.5 13.4 1.0 CD1 A:LEU140 4.5 22.5 1.0 CD1 A:PHE185 4.7 16.6 1.0 SG A:CYS157 4.8 13.5 1.0 N A:CYS193 4.8 13.4 1.0 CA A:LEU191 4.8 13.8 1.0 C A:LEU191 4.8 13.9 1.0 SG A:CYS196 4.8 14.7 1.0

J.Duan, A.Veliju, O.Lampret, L.Liu, S.Yadav, U.P.Apfel, F.A.Armstrong, A.Hemschemeier, E.Hofmann. Insights Into the Molecular Mechanism of Formaldehyde Inhibition of [Fefe]-Hydrogenases J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.3C07800