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Iron in PDB 6yua: Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.

Enzymatic activity of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.

All present enzymatic activity of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion., PDB code: 6yua 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) 39.95 / 3.16
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.333, 89.333, 527.130, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.2

Other elements in 6yua:

The structure of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 4 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. (pdb code 6yua). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion., PDB code: 6yua:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 6yua

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Iron binding site 1 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:0.4
occ:1.00
 FE1 B:SF4701 0.0 0.4 1.0
S4 B:SF4701 2.3 0.7 1.0
S3 B:SF4701 2.3 83.1 1.0
S2 B:SF4701 2.3 0.6 1.0
FE4 B:SF4701 2.6 71.4 1.0
FE2 B:SF4701 2.7 0.5 1.0
FE3 B:SF4701 2.7 0.7 1.0
SG B:CYS38 3.0 0.5 1.0
CB B:CYS38 3.4 0.5 1.0
S1 B:SF4701 3.9 0.2 1.0
N B:GLY41 4.6 0.0 1.0
CB B:PHE40 4.7 0.5 1.0
CA B:CYS38 4.9 0.2 1.0

Iron binding site 2 out of 20 in 6yua

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Iron binding site 2 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:0.5
occ:1.00
 FE2 B:SF4701 0.0 0.5 1.0
S4 B:SF4701 2.3 0.7 1.0
S3 B:SF4701 2.3 83.1 1.0
S1 B:SF4701 2.3 0.2 1.0
FE4 B:SF4701 2.6 71.4 1.0
FE1 B:SF4701 2.7 0.4 1.0
FE3 B:SF4701 2.7 0.7 1.0
SG C:CYS46 3.0 0.5 1.0
CB C:CYS46 3.8 0.0 1.0
S2 B:SF4701 3.9 0.6 1.0
NH1 B:ARG48 4.2 93.1 1.0
CB C:PHE40 4.9 0.4 1.0
NH1 C:ARG48 4.9 75.3 1.0
SG B:CYS46 4.9 0.6 1.0
N C:GLY41 5.0 0.6 1.0

Iron binding site 3 out of 20 in 6yua

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Iron binding site 3 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:0.7
occ:1.00
 FE3 B:SF4701 0.0 0.7 1.0
S4 B:SF4701 2.3 0.7 1.0
S2 B:SF4701 2.3 0.6 1.0
S1 B:SF4701 2.3 0.2 1.0
FE4 B:SF4701 2.6 71.4 1.0
FE1 B:SF4701 2.7 0.4 1.0
FE2 B:SF4701 2.7 0.5 1.0
SG C:CYS38 3.0 0.4 1.0
CB C:CYS38 3.4 1.0 1.0
S3 B:SF4701 3.9 83.1 1.0
NH1 B:ARG56 4.4 0.2 1.0
CB C:PHE40 4.8 0.4 1.0
SG B:CYS38 4.8 0.5 1.0
CA C:CYS38 4.9 0.4 1.0

Iron binding site 4 out of 20 in 6yua

Go back to Iron Binding Sites List in 6yua
Iron binding site 4 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:71.4
occ:1.00
 FE4 B:SF4701 0.0 71.4 1.0
S2 B:SF4701 2.3 0.6 1.0
S1 B:SF4701 2.3 0.2 1.0
S3 B:SF4701 2.3 83.1 1.0
FE3 B:SF4701 2.6 0.7 1.0
FE2 B:SF4701 2.6 0.5 1.0
FE1 B:SF4701 2.6 0.4 1.0
SG B:CYS46 2.9 0.6 1.0
CB B:CYS46 3.8 0.5 1.0
S4 B:SF4701 3.9 0.7 1.0
NH1 C:ARG48 4.6 75.3 1.0

Iron binding site 5 out of 20 in 6yua

Go back to Iron Binding Sites List in 6yua
Iron binding site 5 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:24.4
occ:1.00
 FE1 B:SF4702 0.0 24.4 1.0
S3 B:SF4702 2.3 36.2 1.0
S2 B:SF4702 2.3 0.7 1.0
S4 B:SF4702 2.3 44.6 1.0
FE2 B:SF4702 2.6 43.2 1.0
FE4 B:SF4702 2.7 56.9 1.0
FE3 B:SF4702 2.7 49.5 1.0
SG B:CYS55 2.9 67.7 1.0
CB B:CYS55 3.6 69.1 1.0
S1 B:SF4702 3.9 0.8 1.0
N B:ILE69 4.0 64.6 1.0
CB B:ILE69 4.2 59.7 1.0
N B:GLY53 4.2 96.8 1.0
CA B:GLY53 4.3 99.7 1.0
N B:CYS70 4.5 55.1 1.0
N B:CYS55 4.6 66.5 1.0
CA B:ILE69 4.6 60.5 1.0
CA B:CYS55 4.7 70.4 1.0
CG1 B:ILE69 4.8 61.5 1.0
SG B:CYS50 4.9 82.0 1.0
O B:CYS47 4.9 95.2 1.0
C B:MET52 4.9 94.8 1.0
C B:GLY68 4.9 68.8 1.0
CB B:MET52 4.9 93.6 1.0
CD1 B:ILE69 5.0 61.1 1.0
CA B:GLY68 5.0 71.1 1.0

Iron binding site 6 out of 20 in 6yua

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Iron binding site 6 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:43.2
occ:1.00
 FE2 B:SF4702 0.0 43.2 1.0
S4 B:SF4702 2.3 44.6 1.0
S3 B:SF4702 2.3 36.2 1.0
S1 B:SF4702 2.3 0.8 1.0
FE4 B:SF4702 2.6 56.9 1.0
FE1 B:SF4702 2.6 24.4 1.0
FE3 B:SF4702 2.7 49.5 1.0
SG B:CYS70 2.9 51.6 1.0
CB B:CYS70 3.3 51.4 1.0
N B:CYS70 3.8 55.1 1.0
S2 B:SF4702 3.9 0.7 1.0
CA B:CYS70 4.1 53.5 1.0
CD1 B:ILE196 4.1 53.3 1.0
NH2 B:ARG80 4.3 39.2 1.0
CG1 B:ILE196 4.4 52.6 1.0
N B:ILE69 4.7 64.6 1.0
C B:ILE69 4.9 56.8 1.0
CB B:ALA72 4.9 55.0 1.0

Iron binding site 7 out of 20 in 6yua

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Iron binding site 7 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:49.5
occ:1.00
 FE3 B:SF4702 0.0 49.5 1.0
S4 B:SF4702 2.3 44.6 1.0
S1 B:SF4702 2.3 0.8 1.0
S2 B:SF4702 2.3 0.7 1.0
FE4 B:SF4702 2.6 56.9 1.0
FE2 B:SF4702 2.7 43.2 1.0
FE1 B:SF4702 2.7 24.4 1.0
SG B:CYS47 3.0 97.0 1.0
CB B:CYS47 3.1 98.6 1.0
O B:CYS47 3.9 95.2 1.0
S3 B:SF4702 3.9 36.2 1.0
C B:CYS47 4.0 94.9 1.0
NH2 B:ARG80 4.0 39.2 1.0
CA B:CYS47 4.1 97.3 1.0
N B:ASN49 4.4 84.2 1.0
N B:ARG48 4.6 91.7 1.0
CB B:CYS55 4.7 69.1 1.0
CB B:ASN49 4.8 82.8 1.0
SG B:CYS55 5.0 67.7 1.0

Iron binding site 8 out of 20 in 6yua

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Iron binding site 8 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:56.9
occ:1.00
 FE4 B:SF4702 0.0 56.9 1.0
S2 B:SF4702 2.3 0.7 1.0
S1 B:SF4702 2.3 0.8 1.0
S3 B:SF4702 2.3 36.2 1.0
FE2 B:SF4702 2.6 43.2 1.0
FE3 B:SF4702 2.6 49.5 1.0
FE1 B:SF4702 2.7 24.4 1.0
SG B:CYS50 2.9 82.0 1.0
CB B:CYS50 3.7 81.1 1.0
N B:CYS50 3.8 82.0 1.0
CD1 B:ILE196 3.9 53.3 1.0
S4 B:SF4702 3.9 44.6 1.0
CA B:CYS50 4.2 81.8 1.0
C B:ASN49 4.2 82.4 1.0
N B:ASN49 4.4 84.2 1.0
N B:GLY53 4.6 96.8 1.0
CG1 B:ILE196 4.6 52.6 1.0
C B:CYS50 4.6 83.0 1.0
O B:CYS50 4.6 83.8 1.0
CB B:ILE196 4.7 52.3 1.0
CA B:ASN49 4.7 82.2 1.0
CB B:ASN49 4.8 82.8 1.0
O B:ASN49 4.8 81.5 1.0
CB B:MET52 4.9 93.6 1.0
SG B:CYS47 5.0 97.0 1.0

Iron binding site 9 out of 20 in 6yua

Go back to Iron Binding Sites List in 6yua
Iron binding site 9 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:0.8
occ:1.00
 FE1 B:XCC703 0.0 0.8 1.0
S2 B:XCC703 2.1 0.4 1.0
S3 B:XCC703 2.1 0.6 1.0
S4 B:XCC703 2.2 57.2 1.0
SG B:CYS333 3.1 76.2 1.0
CE1 B:HIS259 3.1 63.1 1.0
FE3 B:XCC703 3.2 0.3 1.0
FE4 B:XCC703 3.3 0.7 1.0
NE2 B:HIS259 3.3 62.4 1.0
CB B:CYS333 3.3 75.9 1.0
FE2 B:XCC703 3.6 0.9 1.0
S1 B:XCC703 3.8 0.0 1.0
NZ B:LYS560 4.2 42.0 1.0
ND1 B:HIS259 4.4 63.6 1.0
NI B:XCC703 4.4 0.5 1.0
CD2 B:HIS259 4.7 62.4 1.0
CB B:CYS294 4.7 53.3 1.0
SG B:CYS294 4.8 53.6 1.0
CD1 B:PHE312 4.8 73.3 1.0
CA B:CYS333 4.8 76.6 1.0
CE B:LYS560 5.0 41.7 1.0

Iron binding site 10 out of 20 in 6yua

Go back to Iron Binding Sites List in 6yua
Iron binding site 10 out of 20 in the Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Co-Dehydrogenase Coupled to the N-Terminal Domain of the Acetyl-Coa Synthase From Clostridium Autoethanogenum Isolated After Tryptic Digestion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:0.9
occ:1.00
 FE2 B:XCC703 0.0 0.9 1.0
S3 B:XCC703 2.1 0.6 1.0
NI B:XCC703 2.7 0.5 1.0
NE2 B:HIS259 3.0 62.4 1.0
CB B:CYS523 3.3 58.3 1.0
SG B:CYS295 3.4 49.5 1.0
NZ B:LYS560 3.4 42.0 1.0
S4 B:XCC703 3.4 57.2 1.0
SG B:CYS523 3.5 59.7 1.0
FE1 B:XCC703 3.6 0.8 1.0
FE4 B:XCC703 3.6 0.7 1.0
S1 B:XCC703 3.6 0.0 1.0
CD2 B:HIS259 3.7 62.4 1.0
CE1 B:HIS259 4.1 63.1 1.0
CE B:LYS560 4.1 41.7 1.0
S2 B:XCC703 4.3 0.4 1.0
CA B:CYS523 4.6 56.0 1.0
CB B:CYS295 4.6 52.6 1.0
CD B:LYS560 4.7 41.5 1.0
FE3 B:XCC703 4.7 0.3 1.0
N B:CYS523 4.8 55.8 1.0
NE2 B:HIS93 4.9 65.5 1.0
CG B:HIS259 5.0 62.4 1.0

Reference:

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
Page generated: Wed Aug 7 16:48:28 2024

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