Iron in PDB 6yu9: Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution

All present enzymatic activity of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution:
1.2.99.2;

The structure of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution, PDB code: 6yu9 was solved by T.Wagner, O.N.Lemaire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.531, 109.446, 129.280, 90.00, 112.55, 90.00
R / Rfree (%)	15.8 / 20.3

The structure of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Chlorine	(Cl)	1 atom

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 Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution (pdb code 6yu9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution, PDB code: 6yu9:
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 Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:14.6 occ:1.00 FE1 A:SF4705 0.0 14.6 1.0 S3 A:SF4705 2.2 17.0 1.0 S4 A:SF4705 2.3 13.8 1.0 SG A:CYS55 2.3 16.6 1.0 S2 A:SF4705 2.4 15.8 1.0 FE3 A:SF4705 2.5 18.6 1.0 FE4 A:SF4705 2.7 14.8 1.0 FE2 A:SF4705 2.8 16.1 1.0 CB A:CYS55 3.1 9.9 1.0 S1 A:SF4705 3.7 16.0 1.0 N A:ILE69 4.1 17.0 1.0 CA A:GLY53 4.2 19.4 1.0 N A:GLY53 4.4 20.1 1.0 CA A:CYS55 4.4 12.3 1.0 N A:CYS55 4.4 13.4 1.0 SG A:CYS47 4.5 17.9 1.0 CB A:CYS47 4.6 17.7 1.0 SG A:CYS50 4.6 18.6 1.0 CA A:GLY68 4.6 18.0 1.0 CB A:ILE69 4.7 15.5 1.0 O A:CYS47 4.8 18.4 1.0 C A:GLY68 4.8 17.5 1.0 N A:CYS70 4.8 21.1 1.0 SG A:CYS70 4.9 15.5 1.0 CA A:ILE69 5.0 16.1 1.0

Iron binding site 2 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:16.1 occ:1.00 FE2 A:SF4705 0.0 16.1 1.0 SG A:CYS70 2.3 15.5 1.0 S4 A:SF4705 2.4 13.8 1.0 S1 A:SF4705 2.4 16.0 1.0 S3 A:SF4705 2.4 17.0 1.0 FE3 A:SF4705 2.7 18.6 1.0 FE1 A:SF4705 2.8 14.6 1.0 FE4 A:SF4705 2.9 14.8 1.0 CB A:CYS70 3.2 20.6 1.0 N A:CYS70 3.9 21.1 1.0 CA A:CYS70 4.1 20.0 1.0 NH2 A:ARG80 4.1 14.5 1.0 S2 A:SF4705 4.3 15.8 1.0 O A:HOH911 4.3 10.0 1.0 CG1 A:ILE196 4.3 11.6 1.0 CB A:ALA72 4.3 11.7 1.0 N A:ILE69 4.7 17.0 1.0 SG A:CYS47 4.8 17.9 1.0 SG A:CYS55 4.8 16.6 1.0 C A:GLY68 4.8 17.5 1.0 SG A:CYS50 4.9 18.6 1.0 N A:ALA72 4.9 11.1 1.0 CA A:GLY68 4.9 18.0 1.0 C A:CYS70 4.9 16.9 1.0 NH1 A:ARG80 5.0 11.8 1.0 N A:GLY71 5.0 13.0 1.0

Iron binding site 3 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:18.6 occ:1.00 FE3 A:SF4705 0.0 18.6 1.0 S1 A:SF4705 2.1 16.0 1.0 SG A:CYS47 2.3 17.9 1.0 S2 A:SF4705 2.3 15.8 1.0 S4 A:SF4705 2.4 13.8 1.0 FE1 A:SF4705 2.5 14.6 1.0 FE4 A:SF4705 2.7 14.8 1.0 FE2 A:SF4705 2.7 16.1 1.0 CB A:CYS47 3.2 17.7 1.0 NH2 A:ARG80 3.7 14.5 1.0 S3 A:SF4705 3.8 17.0 1.0 N A:ASN49 4.1 18.9 1.0 C A:CYS47 4.3 19.6 1.0 CB A:ASN49 4.3 15.7 1.0 CA A:CYS47 4.4 18.8 1.0 O A:CYS47 4.4 18.4 1.0 SG A:CYS55 4.5 16.6 1.0 CB A:CYS55 4.5 9.9 1.0 N A:ARG48 4.6 21.1 1.0 CA A:ASN49 4.6 17.2 1.0 N A:CYS50 4.8 17.7 1.0 CZ A:ARG80 4.8 15.4 1.0 SG A:CYS50 4.9 18.6 1.0 SG A:CYS70 4.9 15.5 1.0 C A:ASN49 4.9 18.9 1.0

Iron binding site 4 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:14.8 occ:1.00 FE4 A:SF4705 0.0 14.8 1.0 SG A:CYS50 2.2 18.6 1.0 S1 A:SF4705 2.3 16.0 1.0 S2 A:SF4705 2.5 15.8 1.0 S3 A:SF4705 2.5 17.0 1.0 FE1 A:SF4705 2.7 14.6 1.0 FE3 A:SF4705 2.7 18.6 1.0 FE2 A:SF4705 2.9 16.1 1.0 CB A:CYS50 3.3 16.2 1.0 N A:CYS50 3.8 17.7 1.0 CA A:CYS50 4.0 16.9 1.0 S4 A:SF4705 4.1 13.8 1.0 CG1 A:ILE196 4.1 11.6 1.0 O A:CYS50 4.1 17.8 1.0 N A:GLY53 4.3 20.1 1.0 C A:CYS50 4.3 17.4 1.0 C A:ASN49 4.3 18.9 1.0 CB A:MET52 4.5 20.4 1.0 CE A:MET52 4.6 19.2 1.0 CB A:ILE196 4.7 11.9 1.0 N A:ASN49 4.7 18.9 1.0 N A:MET52 4.8 22.0 1.0 SG A:CYS55 4.8 16.6 1.0 CA A:GLY53 4.8 19.4 1.0 SG A:CYS47 4.8 17.9 1.0 O A:ASN49 4.9 20.2 1.0 SG A:CYS70 4.9 15.5 1.0 CA A:ASN49 4.9 17.2 1.0 C A:MET52 5.0 22.7 1.0

Iron binding site 5 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:22.2 occ:1.00 FE1 A:XCC706 0.0 22.2 1.0 S3 A:XCC706 2.3 23.3 1.0 SG A:CYS333 2.3 12.7 1.0 S2 A:XCC706 2.3 24.7 1.0 S4 A:XCC706 2.3 22.9 1.0 FE3 A:XCC706 2.8 25.9 1.0 FE4 A:XCC706 2.9 25.4 1.0 NI A:XCC706 3.0 40.8 1.0 CB A:CYS333 3.2 12.0 1.0 FE2 A:XCC706 3.3 27.6 1.0 NE2 A:HIS259 3.8 23.5 1.0 S1 A:XCC706 3.8 28.2 1.0 NZ A:LYS560 3.9 14.9 1.0 CE1 A:HIS259 4.0 24.1 1.0 O A:HOH995 4.2 43.4 1.0 CE A:LYS560 4.5 14.4 1.0 CA A:CYS333 4.7 15.5 1.0 CE A:MET557 4.7 33.1 1.0 SG A:CYS451 4.8 14.2 1.0 CB A:CYS451 5.0 13.0 1.0 OG A:SER558 5.0 15.4 1.0

Iron binding site 6 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:27.6 occ:1.00 FE2 A:XCC706 0.0 27.6 1.0 NE2 A:HIS259 2.2 23.5 1.0 SG A:CYS295 2.2 24.9 1.0 S3 A:XCC706 2.3 23.3 1.0 NI A:XCC706 2.8 40.8 1.0 O A:HOH995 2.9 43.4 1.0 CD2 A:HIS259 2.9 22.1 1.0 FE1 A:XCC706 3.3 22.2 1.0 CE1 A:HIS259 3.3 24.1 1.0 CB A:CYS295 3.3 19.2 1.0 SG A:CYS523 3.3 22.5 1.0 NZ A:LYS560 3.9 14.9 1.0 FE4 A:XCC706 4.0 25.4 1.0 S4 A:XCC706 4.0 22.9 1.0 CG A:HIS259 4.1 22.7 1.0 CB A:CYS523 4.1 17.3 1.0 O A:HOH898 4.1 12.5 1.0 S1 A:XCC706 4.2 28.2 1.0 ND1 A:HIS259 4.2 23.9 1.0 O A:HOH960 4.2 19.2 1.0 N A:CYS295 4.3 17.8 1.0 CA A:CYS295 4.4 18.3 1.0 O A:HOH987 4.5 18.5 1.0 SG A:CYS333 4.7 12.7 1.0 FE3 A:XCC706 4.8 25.9 1.0 N A:CYS523 4.9 15.8 1.0 CE A:LYS560 4.9 14.4 1.0

Iron binding site 7 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:25.9 occ:1.00 FE3 A:XCC706 0.0 25.9 1.0 S2 A:XCC706 2.2 24.7 1.0 SG A:CYS451 2.4 14.2 1.0 S4 A:XCC706 2.4 22.9 1.0 S1 A:XCC706 2.4 28.2 1.0 NI A:XCC706 2.7 40.8 1.0 CB A:CYS451 2.7 13.0 1.0 FE1 A:XCC706 2.8 22.2 1.0 FE4 A:XCC706 2.9 25.4 1.0 CA A:CYS451 3.2 12.6 1.0 N A:CYS451 3.3 11.3 1.0 S3 A:XCC706 4.0 23.3 1.0 C A:GLY450 4.1 11.8 1.0 OG A:SER558 4.1 15.4 1.0 CE A:MET557 4.3 33.1 1.0 SG A:CYS333 4.6 12.7 1.0 CA A:GLY450 4.6 11.9 1.0 CB A:SER558 4.6 10.3 1.0 C A:CYS451 4.7 15.1 1.0 O A:GLY450 4.8 11.6 1.0 FE2 A:XCC706 4.8 27.6 1.0 SG A:CYS481 4.9 18.5 1.0 O A:HOH995 4.9 43.4 1.0 SG A:CYS523 5.0 22.5 1.0

Iron binding site 8 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:25.4 occ:1.00 FE4 A:XCC706 0.0 25.4 1.0 S2 A:XCC706 2.3 24.7 1.0 S3 A:XCC706 2.3 23.3 1.0 S1 A:XCC706 2.3 28.2 1.0 SG A:CYS481 2.3 18.5 1.0 FE3 A:XCC706 2.9 25.9 1.0 FE1 A:XCC706 2.9 22.2 1.0 NI A:XCC706 3.4 40.8 1.0 CB A:CYS481 3.4 11.8 1.0 O A:HOH960 3.9 19.2 1.0 N A:CYS481 3.9 13.6 1.0 FE2 A:XCC706 4.0 27.6 1.0 CA A:CYS451 4.1 12.6 1.0 CB A:PHE312 4.2 21.0 1.0 CA A:CYS481 4.3 13.5 1.0 S4 A:XCC706 4.3 22.9 1.0 CB A:CYS451 4.4 13.0 1.0 SG A:CYS294 4.5 19.5 1.0 N A:CYS451 4.6 11.3 1.0 CB A:CYS294 4.8 16.9 1.0 O A:GLY450 4.8 11.6 1.0 C A:GLY450 4.9 11.8 1.0 SG A:CYS523 4.9 22.5 1.0 C A:GLY480 4.9 14.3 1.0 CG A:PHE312 4.9 21.0 1.0

Iron binding site 9 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:24.3 occ:1.00 FE1 B:SF4702 0.0 24.3 1.0 SG A:CYS38 2.2 21.5 1.0 S2 B:SF4702 2.3 20.8 1.0 S3 B:SF4702 2.3 23.5 1.0 S4 B:SF4702 2.4 21.8 1.0 FE3 B:SF4702 2.7 21.0 1.0 FE4 B:SF4702 2.8 24.8 1.0 FE2 B:SF4702 2.8 22.5 1.0 CB A:CYS38 3.2 19.1 1.0 S1 B:SF4702 4.1 19.8 1.0 N A:GLY41 4.3 19.7 1.0 CB A:PHE40 4.5 24.5 1.0 CA A:CYS38 4.6 21.2 1.0 NH1 B:ARG56 4.7 62.3 1.0 SG B:CYS38 4.7 27.7 1.0 SG A:CYS46 4.7 21.4 1.0 CB A:CYS46 4.8 20.5 1.0 CA A:GLY41 4.9 20.8 1.0 O B:HOH964 4.9 12.0 1.0 SG B:CYS46 4.9 23.5 1.0

Iron binding site 10 out of 40 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:22.5 occ:1.00 FE2 B:SF4702 0.0 22.5 1.0 S3 B:SF4702 2.2 23.5 1.0 SG B:CYS46 2.3 23.5 1.0 S4 B:SF4702 2.3 21.8 1.0 S1 B:SF4702 2.5 19.8 1.0 FE4 B:SF4702 2.5 24.8 1.0 FE3 B:SF4702 2.7 21.0 1.0 FE1 B:SF4702 2.8 24.3 1.0 CB B:CYS46 3.1 20.3 1.0 NH1 A:ARG48 3.4 27.9 1.0 S2 B:SF4702 3.9 20.8 1.0 O B:HOH964 4.0 12.0 1.0 NH1 B:ARG48 4.2 34.4 1.0 SG A:CYS46 4.5 21.4 1.0 CA B:CYS46 4.6 21.0 1.0 CZ A:ARG48 4.7 30.9 1.0 SG B:CYS38 4.7 27.7 1.0 SG A:CYS38 4.8 21.5 1.0 N B:GLY41 5.0 22.4 1.0

O.N.Lemaire, T.Wagner. Gas Channel Rerouting in A Primordial Enzyme: Structural Insights of the Carbon-Monoxide Dehydrogenase/Acetyl-Coa Synthase Complex From the Acetogen Clostridium Autoethanogenum. Biochim Biophys Acta V.1862 48330 2020BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 33080205
DOI: 10.1016/J.BBABIO.2020.148330