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Nickel 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:

Magnesium (Mg) 4 atoms
Iron (Fe) 20 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel 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 Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6yua

Go back to Nickel Binding Sites List in 6yua
Nickel binding site 1 out of 2 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 Nickel with other atoms in the Ni 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:Ni703

b:0.5
occ:1.00
 NI B:XCC703 0.0 0.5 1.0
S1 B:XCC703 2.3 0.0 1.0
FE2 B:XCC703 2.7 0.9 1.0
S4 B:XCC703 3.0 57.2 1.0
SG B:CYS523 3.1 59.7 1.0
FE3 B:XCC703 3.6 0.3 1.0
S3 B:XCC703 3.7 0.6 1.0
FE4 B:XCC703 3.8 0.7 1.0
CB B:CYS523 3.9 58.3 1.0
OG B:SER558 4.0 59.6 1.0
SG B:CYS451 4.0 62.4 1.0
S2 B:XCC703 4.3 0.4 1.0
CD1 B:ILE564 4.4 35.6 1.0
FE1 B:XCC703 4.4 0.8 1.0
CB B:LYS560 4.8 43.2 1.0
CE B:LYS560 4.8 41.7 1.0
NZ B:LYS560 4.9 42.0 1.0
O B:GLY450 5.0 58.4 1.0
N B:ALA561 5.0 42.5 1.0

Nickel binding site 2 out of 2 in 6yua

Go back to Nickel Binding Sites List in 6yua
Nickel binding site 2 out of 2 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 Nickel with other atoms in the Ni 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
C:Ni704

b:0.3
occ:1.00
 NI C:XCC704 0.0 0.3 1.0
S1 C:XCC704 2.3 97.5 1.0
FE2 C:XCC704 2.6 95.4 1.0
S4 C:XCC704 2.9 88.7 1.0
SG C:CYS295 3.0 59.3 1.0
SG C:CYS523 3.1 73.3 1.0
CB C:CYS523 3.3 74.0 1.0
FE3 C:XCC704 3.5 96.8 1.0
S3 C:XCC704 3.6 96.2 1.0
FE4 C:XCC704 3.8 95.1 1.0
NE2 C:HIS259 3.9 56.3 1.0
S2 C:XCC704 4.3 96.3 1.0
FE1 C:XCC704 4.3 95.6 1.0
N C:CYS523 4.3 70.8 1.0
CA C:GLY480 4.3 48.0 1.0
CA C:CYS523 4.4 72.5 1.0
CB C:CYS295 4.5 58.9 1.0
CE1 C:HIS259 4.7 57.2 1.0
NZ C:LYS560 4.8 37.2 1.0
CD2 C:HIS259 4.8 56.9 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: Thu Oct 10 09:02:22 2024

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