Iron in PDB 6ytt: Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution

All present enzymatic activity of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution:
1.2.99.2; 2.3.1.169;

The structure of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution, PDB code: 6ytt 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)	49.15 / 3.01
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	298.943, 298.943, 128.895, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22

The structure of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Nickel	(Ni)	6 atoms
Sodium	(Na)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution (pdb code 6ytt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution, PDB code: 6ytt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe804 b:0.2 occ:1.00 FE1 A:SF4804 0.0 0.2 1.0 S2 A:SF4804 2.3 0.7 1.0 S3 A:SF4804 2.3 0.2 1.0 S4 A:SF4804 2.3 0.2 1.0 FE2 A:SF4804 2.6 0.9 1.0 FE4 A:SF4804 2.6 0.5 1.0 FE3 A:SF4804 2.7 0.8 1.0 SG A:CYS485 2.9 0.1 1.0 CB A:CYS485 3.3 0.8 1.0 S1 A:SF4804 3.9 0.1 1.0 N A:LEU487 4.1 1.0 1.0 C A:CYS485 4.1 0.3 1.0 CB A:LEU487 4.2 0.7 1.0 O A:CYS485 4.3 0.8 1.0 CA A:CYS485 4.3 0.5 1.0 N A:CYS488 4.5 0.0 1.0 N A:ASN486 4.5 0.8 1.0 CA A:LEU487 4.7 1.0 1.0 NI A:NI808 4.8 0.1 1.0 CB A:CYS497 4.8 0.3 1.0 CB A:CYS488 4.9 0.2 1.0 C A:ASN486 5.0 0.2 1.0

Iron binding site 2 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe804 b:0.9 occ:1.00 FE2 A:SF4804 0.0 0.9 1.0 S1 A:SF4804 2.3 0.1 1.0 S4 A:SF4804 2.3 0.2 1.0 S3 A:SF4804 2.3 0.2 1.0 FE1 A:SF4804 2.6 0.2 1.0 FE4 A:SF4804 2.6 0.5 1.0 FE3 A:SF4804 2.7 0.8 1.0 SG A:CYS497 2.8 0.5 1.0 CB A:CYS497 3.2 0.3 1.0 NI A:NI808 3.8 0.1 1.0 S2 A:SF4804 3.9 0.7 1.0 NE2 A:HIS495 4.3 0.9 1.0 CA A:CYS497 4.6 0.4 1.0 SG A:CYS574 4.6 0.5 1.0 CG A:LEU506 4.7 0.5 1.0 CB A:CYS485 4.8 0.8 1.0 N A:CYS497 4.8 0.8 1.0 CD2 A:HIS495 4.8 99.0 1.0 N A:LEU506 4.8 97.5 1.0 SG A:CYS507 4.9 95.1 1.0 O A:CYS485 5.0 0.8 1.0

Iron binding site 3 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe804 b:0.8 occ:1.00 FE3 A:SF4804 0.0 0.8 1.0 S2 A:SF4804 2.3 0.7 1.0 S4 A:SF4804 2.3 0.2 1.0 S1 A:SF4804 2.3 0.1 1.0 FE2 A:SF4804 2.7 0.9 1.0 FE4 A:SF4804 2.7 0.5 1.0 FE1 A:SF4804 2.7 0.2 1.0 SG A:CYS507 2.9 95.1 1.0 NH1 A:ARG383 3.6 0.5 1.0 CB A:CYS507 3.7 84.3 1.0 S3 A:SF4804 3.9 0.2 1.0 NI A:NI808 4.1 0.1 1.0 CG2 A:VAL510 4.3 88.5 1.0 N A:CYS507 4.6 87.3 1.0 CB A:VAL510 4.6 88.1 1.0 CA A:CYS507 4.8 87.4 1.0 CZ A:ARG383 4.9 0.7 1.0 SG A:CYS576 5.0 95.0 1.0

Iron binding site 4 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe804 b:0.5 occ:1.00 FE4 A:SF4804 0.0 0.5 1.0 NI A:NI808 2.2 0.1 1.0 S1 A:SF4804 2.3 0.1 1.0 S2 A:SF4804 2.3 0.7 1.0 S3 A:SF4804 2.3 0.2 1.0 FE2 A:SF4804 2.6 0.9 1.0 FE1 A:SF4804 2.6 0.2 1.0 FE3 A:SF4804 2.7 0.8 1.0 SG A:CYS488 2.9 0.1 1.0 CB A:CYS488 3.1 0.2 1.0 S4 A:SF4804 3.9 0.2 1.0 N A:CYS488 4.0 0.0 1.0 SG A:CYS574 4.0 0.5 1.0 CA A:CYS488 4.2 0.6 1.0 SG A:CYS576 4.2 95.0 1.0 OH A:TYR387 4.6 0.2 1.0 CB A:CYS574 4.9 98.8 1.0 SG A:CYS497 5.0 0.5 1.0

Iron binding site 5 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe707 b:94.0 occ:1.00 FE1 B:SF4707 0.0 94.0 1.0 S2 B:SF4707 2.3 0.5 1.0 S3 B:SF4707 2.3 0.8 1.0 S4 B:SF4707 2.3 0.9 1.0 FE4 B:SF4707 2.6 89.3 1.0 FE2 B:SF4707 2.6 84.2 1.0 FE3 B:SF4707 2.7 87.7 1.0 SG B:CYS38 2.9 0.0 1.0 CB B:CYS38 3.2 61.0 1.0 S1 B:SF4707 3.9 0.5 1.0 N B:GLY41 4.4 62.7 1.0 CB B:PHE40 4.4 63.8 1.0 CA B:CYS38 4.7 60.9 1.0 NH1 C:ARG56 4.9 0.5 1.0 CD2 B:PHE40 5.0 97.2 1.0 CA B:GLY41 5.0 55.7 1.0

Iron binding site 6 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe707 b:84.2 occ:1.00 FE2 B:SF4707 0.0 84.2 1.0 S4 B:SF4707 2.3 0.9 1.0 S1 B:SF4707 2.3 0.5 1.0 S3 B:SF4707 2.3 0.8 1.0 FE4 B:SF4707 2.6 89.3 1.0 FE1 B:SF4707 2.6 94.0 1.0 FE3 B:SF4707 2.7 87.7 1.0 SG C:CYS46 2.8 64.3 1.0 CB C:CYS46 3.5 44.1 1.0 S2 B:SF4707 3.9 0.5 1.0 NH1 B:ARG48 4.0 88.3 1.0 NH1 C:ARG48 4.8 0.6 1.0 SG B:CYS46 4.9 63.4 1.0 N C:GLY41 5.0 57.0 1.0

Iron binding site 7 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe707 b:87.7 occ:1.00 FE3 B:SF4707 0.0 87.7 1.0 S4 B:SF4707 2.3 0.9 1.0 S2 B:SF4707 2.3 0.5 1.0 S1 B:SF4707 2.3 0.5 1.0 FE4 B:SF4707 2.6 89.3 1.0 FE2 B:SF4707 2.7 84.2 1.0 FE1 B:SF4707 2.7 94.0 1.0 SG C:CYS38 2.8 82.2 1.0 CB C:CYS38 3.3 59.3 1.0 S3 B:SF4707 3.9 0.8 1.0 NH1 B:ARG56 4.6 84.8 1.0 N C:GLY41 4.6 57.0 1.0 SG B:CYS38 4.7 0.0 1.0 CB C:PHE40 4.7 47.2 1.0 F C:F1006 4.8 39.6 1.0 CA C:CYS38 4.8 57.8 1.0

Iron binding site 8 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe707 b:89.3 occ:1.00 FE4 B:SF4707 0.0 89.3 1.0 S2 B:SF4707 2.3 0.5 1.0 S3 B:SF4707 2.3 0.8 1.0 S1 B:SF4707 2.3 0.5 1.0 FE3 B:SF4707 2.6 87.7 1.0 FE1 B:SF4707 2.6 94.0 1.0 FE2 B:SF4707 2.6 84.2 1.0 SG B:CYS46 2.8 63.4 1.0 CB B:CYS46 3.5 49.3 1.0 S4 B:SF4707 3.9 0.9 1.0 NH1 C:ARG48 4.3 0.6 1.0 NH1 B:ARG48 4.7 88.3 1.0 CA B:CYS46 4.9 48.5 1.0 CB B:PHE40 5.0 63.8 1.0

Iron binding site 9 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe708 b:0.1 occ:1.00 FE1 B:SF4708 0.0 0.1 1.0 S3 B:SF4708 2.3 1.0 1.0 S2 B:SF4708 2.3 0.4 1.0 S4 B:SF4708 2.3 0.3 1.0 FE2 B:SF4708 2.6 0.5 1.0 FE4 B:SF4708 2.6 98.2 1.0 FE3 B:SF4708 2.7 0.1 1.0 SG B:CYS55 2.8 91.1 1.0 CB B:CYS55 3.2 58.9 1.0 S1 B:SF4708 3.9 0.5 1.0 N B:ILE69 4.1 56.4 1.0 CA B:GLY53 4.3 67.1 1.0 N B:CYS55 4.4 62.4 1.0 CA B:CYS55 4.4 52.3 1.0 N B:GLY53 4.4 71.4 1.0 CB B:ILE69 4.6 56.7 1.0 N B:CYS70 4.7 55.5 1.0 CA B:GLY68 4.7 53.6 1.0 O B:CYS47 4.8 65.1 1.0 SG B:CYS50 4.9 54.3 1.0 C B:GLY68 4.9 58.4 1.0 CA B:ILE69 4.9 57.1 1.0 CB B:CYS47 5.0 46.0 1.0 C B:MET52 5.0 63.5 1.0

Iron binding site 10 out of 28 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe708 b:0.5 occ:1.00 FE2 B:SF4708 0.0 0.5 1.0 S4 B:SF4708 2.3 0.3 1.0 S3 B:SF4708 2.3 1.0 1.0 S1 B:SF4708 2.3 0.5 1.0 FE4 B:SF4708 2.6 98.2 1.0 FE1 B:SF4708 2.6 0.1 1.0 FE3 B:SF4708 2.6 0.1 1.0 SG B:CYS70 2.8 69.4 1.0 CB B:CYS70 3.2 53.8 1.0 N B:CYS70 3.7 55.5 1.0 S2 B:SF4708 3.9 0.4 1.0 CA B:CYS70 4.1 56.0 1.0 CD1 B:ILE196 4.5 0.6 1.0 NH2 B:ARG80 4.5 78.9 1.0 N B:ILE69 4.6 56.4 1.0 CB B:ALA72 4.6 55.5 1.0 CG1 B:ILE196 4.7 68.2 1.0 C B:GLY68 4.9 58.4 1.0 C B:ILE69 4.9 57.4 1.0 C B:CYS70 4.9 70.4 1.0 CA B:GLY68 4.9 53.6 1.0 SG B:CYS50 5.0 54.3 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