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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6ytt:

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

Nickel (Ni) 6 atoms
Iron (Fe) 28 atoms
Sodium (Na) 6 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 9 in 6ytt

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Fluorine binding site 1 out of 9 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 Fluorine with other atoms in the F 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:F805

b:50.5
occ:1.00
 NZ A:LYS99 3.5 61.8 1.0
CD A:LYS99 3.8 57.5 1.0
CE1 A:TYR107 4.0 91.3 1.0
CE A:LYS99 4.0 55.9 1.0
CZ A:TYR107 4.2 80.6 1.0
OD2 A:ASP191 4.3 1.0 1.0
OH A:TYR107 4.3 80.3 1.0
O A:PRO106 4.4 70.9 1.0
CD1 A:TYR107 4.6 80.8 1.0
CE2 A:TYR107 4.9 61.8 1.0

Fluorine binding site 2 out of 9 in 6ytt

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Fluorine binding site 2 out of 9 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 Fluorine with other atoms in the F 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:F806

b:88.3
occ:1.00
 NE2 A:HIS386 2.5 0.8 1.0
CE1 A:HIS386 3.4 0.4 1.0
CD2 A:HIS386 3.5 0.5 1.0
SG A:CYS488 4.2 0.1 1.0
CE1 A:PHE491 4.4 99.9 1.0
OH A:TYR387 4.5 0.2 1.0
ND1 A:HIS386 4.6 0.1 1.0
CZ A:TYR387 4.6 0.4 1.0
CG A:HIS386 4.6 0.6 1.0
CB A:CYS576 4.6 84.2 1.0
OE2 A:GLU306 4.8 0.5 1.0
CE2 A:TYR387 4.9 0.7 1.0
CZ A:PHE491 4.9 91.8 1.0
SG A:CYS576 5.0 95.0 1.0
CE1 A:TYR387 5.0 0.2 1.0

Fluorine binding site 3 out of 9 in 6ytt

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Fluorine binding site 3 out of 9 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 Fluorine with other atoms in the F 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
B:F710

b:33.6
occ:1.00
 ND1 B:HIS346 3.0 68.8 1.0
O B:GLY322 3.5 64.6 1.0
CE1 B:HIS346 3.7 76.0 1.0
N B:ASP390 3.9 78.8 1.0
CA B:GLY322 4.0 74.6 1.0
CG B:HIS346 4.1 51.5 1.0
O B:ASP390 4.2 89.3 1.0
CB B:ASP390 4.2 69.6 1.0
C B:GLY322 4.2 69.5 1.0
N B:HIS346 4.4 51.8 1.0
CA B:ASP390 4.5 82.6 1.0
CB B:HIS346 4.5 50.9 1.0
CG B:ARG389 4.7 75.1 1.0
CD1 B:TYR345 4.7 45.2 1.0
C B:ASP390 4.8 84.7 1.0
CB B:LYS393 4.8 77.8 1.0
NE2 B:HIS346 4.8 58.4 1.0
CA B:ARG389 4.9 56.4 1.0
C B:ARG389 4.9 71.4 1.0
CB B:TYR345 5.0 54.2 1.0

Fluorine binding site 4 out of 9 in 6ytt

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Fluorine binding site 4 out of 9 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 Fluorine with other atoms in the F 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
C:F1006

b:39.6
occ:1.00
 NH1 C:ARG56 3.4 0.5 1.0
NH1 B:ARG56 3.7 84.8 1.0
SG B:CYS38 4.1 0.0 1.0
SG C:CYS38 4.3 82.2 1.0
CZ C:ARG56 4.7 96.4 1.0
S4 B:SF4707 4.7 0.9 1.0
FE3 B:SF4707 4.8 87.7 1.0
CZ B:ARG56 4.8 74.8 1.0
S2 B:SF4707 5.0 0.5 1.0

Fluorine binding site 5 out of 9 in 6ytt

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Fluorine binding site 5 out of 9 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 Fluorine with other atoms in the F 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
C:F1007

b:76.3
occ:1.00
 CD C:LYS207 3.3 57.9 1.0
NZ C:LYS207 3.4 79.8 1.0
CE C:LYS207 4.0 67.8 1.0
CA C:ALA204 4.5 56.4 1.0
CG C:LYS207 4.6 43.6 1.0
CB C:ALA204 4.7 73.2 1.0
CB C:LYS207 4.8 52.3 1.0
CE1 B:HIS357 5.0 73.9 1.0
N C:ALA204 5.0 51.1 1.0

Fluorine binding site 6 out of 9 in 6ytt

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Fluorine binding site 6 out of 9 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 Fluorine with other atoms in the F 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
C:F1008

b:52.0
occ:1.00
 NZ C:LYS628 3.1 93.5 1.0
OE2 C:GLU598 3.2 0.9 1.0
CG C:GLU598 4.0 88.1 1.0
CD C:GLU598 4.1 0.6 1.0
O C:GLY602 4.2 60.7 1.0
CE C:LYS625 4.3 71.9 1.0
CE C:LYS628 4.3 95.9 1.0
NH2 C:ARG621 4.4 85.0 1.0
CD C:LYS628 4.6 86.1 1.0
C C:GLY602 4.9 54.6 1.0
CZ C:ARG621 4.9 80.6 1.0
CA C:GLY602 4.9 65.8 1.0
NH1 C:ARG621 5.0 91.2 1.0

Fluorine binding site 7 out of 9 in 6ytt

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Fluorine binding site 7 out of 9 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 Fluorine with other atoms in the F 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
C:F1009

b:51.1
occ:1.00
 NH1 C:ARG181 3.3 58.4 1.0
CG B:LYS355 3.7 49.2 1.0
CE B:LYS355 3.7 84.4 1.0
NH2 C:ARG181 3.7 53.9 1.0
NH1 C:ARG185 3.9 83.2 1.0
CZ C:ARG181 4.0 56.0 1.0
CD B:LYS355 4.2 62.6 1.0
CZ C:ARG185 4.5 71.9 1.0
OD2 B:ASP95 4.7 82.0 1.0
CB C:ALA189 4.9 44.1 1.0
CB B:LYS355 5.0 35.7 1.0
NH2 C:ARG185 5.0 79.0 1.0

Fluorine binding site 8 out of 9 in 6ytt

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Fluorine binding site 8 out of 9 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 Fluorine with other atoms in the F 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
C:F1010

b:41.8
occ:1.00
 ND1 C:HIS346 3.3 89.3 1.0
O C:GLY322 3.5 92.6 1.0
CA C:GLY322 3.9 88.3 1.0
CE1 C:HIS346 4.0 96.5 1.0
O C:ASP390 4.1 0.0 1.0
CE C:LYS393 4.1 0.7 1.0
C C:GLY322 4.2 92.7 1.0
N C:ASP390 4.2 99.0 1.0
CG C:HIS346 4.3 90.5 1.0
N C:HIS346 4.4 93.9 1.0
CB C:ASP390 4.5 97.8 1.0
CD1 C:TYR345 4.5 86.3 1.0
CB C:HIS346 4.6 97.4 1.0
CB C:TYR345 4.8 96.5 1.0
CA C:ASP390 4.8 0.2 1.0
CB C:LYS393 4.8 0.2 1.0
C C:ASP390 4.9 0.5 1.0
CD C:LYS393 4.9 0.8 1.0
CA C:TYR345 4.9 96.8 1.0

Fluorine binding site 9 out of 9 in 6ytt

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Fluorine binding site 9 out of 9 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 Fluorine with other atoms in the F 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
C:F1011

b:70.6
occ:1.00
 NE2 C:HIS236 3.0 0.2 1.0
CB C:GLU410 3.6 93.8 1.0
CE1 C:HIS236 3.6 0.1 1.0
CG C:GLU410 4.0 0.5 1.0
CG2 C:THR234 4.1 63.0 1.0
CB C:THR234 4.1 75.1 1.0
CD2 C:HIS236 4.2 0.2 1.0
OD2 C:ASP117 4.4 0.3 1.0
OG1 C:THR234 4.6 91.4 1.0
ND2 C:ASN414 4.8 78.9 1.0
ND1 C:HIS236 4.8 0.6 1.0
CA C:GLU410 4.9 85.9 1.0
CD C:GLU410 4.9 0.6 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: Sun Dec 13 13:42:49 2020

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