Sodium 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:

Fluorine (F) 9 atoms
Nickel (Ni) 6 atoms
Iron (Fe) 28 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 6 in 6ytt

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Sodium binding site 1 out of 6 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 Sodium with other atoms in the Na 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
B:Na711

b:1.0
occ:1.00
OE1 B:GLU226 2.8 0.9 1.0
CD B:GLU226 4.0 90.4 1.0
NH2 B:ARG535 4.5 84.3 1.0
OD2 B:ASP531 4.7 71.1 1.0
CG B:GLU226 4.7 72.7 1.0
CG2 B:VAL124 4.8 45.9 1.0
CD B:PRO163 4.9 48.8 1.0
OE2 B:GLU226 4.9 84.5 1.0
CE1 B:PHE222 4.9 40.5 1.0
CE B:LYS120 5.0 80.3 1.0

Sodium binding site 2 out of 6 in 6ytt

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Sodium binding site 2 out of 6 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 Sodium with other atoms in the Na 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
B:Na712

b:63.2
occ:1.00
O B:TYR345 2.7 73.6 1.0
O B:SER342 2.9 44.2 1.0
O B:THR347 3.0 79.4 1.0
C B:SER342 4.0 47.0 1.0
C B:TYR345 4.0 57.5 1.0
C B:HIS346 4.0 62.0 1.0
C B:THR347 4.0 60.8 1.0
N B:THR347 4.2 48.6 1.0
O B:HIS346 4.3 75.7 1.0
CA B:HIS346 4.3 63.1 1.0
CA B:LYS343 4.4 54.6 1.0
N B:LYS343 4.6 47.5 1.0
N B:HIS346 4.7 51.8 1.0
CA B:THR347 4.7 48.3 1.0
C B:LYS343 4.8 59.7 1.0
O B:LYS343 4.9 66.2 1.0
N B:TYR345 4.9 45.8 1.0
CB B:SER342 4.9 45.6 1.0

Sodium binding site 3 out of 6 in 6ytt

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Sodium binding site 3 out of 6 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 Sodium with other atoms in the Na 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:Na713

b:63.0
occ:1.00
OD1 B:ASN595 3.6 0.3 1.0
OD2 B:ASP599 4.0 94.9 1.0
ND2 B:ASN595 4.0 81.3 1.0
OD1 B:ASP599 4.1 93.5 1.0
CG B:ASN595 4.2 83.6 1.0
CG B:ASP599 4.4 93.6 1.0
OE2 B:GLU598 4.9 91.6 1.0

Sodium binding site 4 out of 6 in 6ytt

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Sodium binding site 4 out of 6 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 Sodium with other atoms in the Na 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:Na1012

b:56.4
occ:1.00
OE1 C:GLU608 3.8 0.9 1.0
OG1 C:THR609 4.4 81.1 1.0
OE2 C:GLU608 4.5 0.7 1.0
CD C:GLU608 4.5 0.1 1.0

Sodium binding site 5 out of 6 in 6ytt

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Sodium binding site 5 out of 6 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 Sodium with other atoms in the Na 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:Na1013

b:84.2
occ:1.00
OE2 C:GLU226 2.7 0.5 1.0
CD C:GLU226 3.9 0.6 1.0
NH2 C:ARG535 4.4 97.5 1.0
OD2 C:ASP531 4.6 78.8 1.0
CG C:GLU226 4.7 98.3 1.0
CE1 C:PHE222 4.8 61.1 1.0
CD C:PRO163 4.9 64.4 1.0
OE1 C:GLU226 4.9 96.0 1.0
CG2 C:VAL124 5.0 80.0 1.0

Sodium binding site 6 out of 6 in 6ytt

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Sodium binding site 6 out of 6 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 Sodium with other atoms in the Na 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:Na1014

b:80.0
occ:1.00
OD2 C:ASP599 3.6 89.4 1.0
ND2 C:ASN595 3.6 90.6 1.0
OD1 C:ASN595 3.6 0.9 1.0
CG C:ASN595 4.0 82.8 1.0
OD1 C:ASP599 4.2 88.8 1.0
CG C:ASP599 4.3 90.8 1.0
O C:ASN595 4.9 92.3 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: Tue Dec 15 16:38:13 2020

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