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Magnesium 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
Iron (Fe) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6yua

Go back to Magnesium Binding Sites List in 6yua
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg401

b:37.5
occ:1.00
 NH1 A:ARG184 2.8 0.1 1.0
OD2 A:ASP131 3.1 95.8 1.0
CG A:ASP131 4.0 95.8 1.0
CZ A:ARG184 4.0 0.0 1.0
OD1 A:ASP131 4.3 96.7 1.0
CD A:ARG184 4.4 91.2 1.0
NE A:ARG184 4.6 95.4 1.0
O A:GLY159 4.7 75.0 1.0
O A:ASP131 4.9 90.8 1.0
CG2 A:ILE132 4.9 80.7 1.0
NH2 A:ARG184 4.9 0.3 1.0

Magnesium binding site 2 out of 4 in 6yua

Go back to Magnesium Binding Sites List in 6yua
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg704

b:33.6
occ:1.00
 OD2 B:ASP531 3.3 31.7 1.0
CG B:ARG528 3.7 36.9 1.0
NZ B:LYS120 3.9 68.6 1.0
CA B:ARG528 4.1 36.8 1.0
CG B:ASP531 4.1 31.7 1.0
CB B:ASP531 4.2 33.2 1.0
CG2 B:THR225 4.2 47.0 1.0
CB B:ARG528 4.3 37.2 1.0
CG2 B:VAL409 4.4 41.7 1.0
NH2 B:ARG528 4.4 40.1 1.0
N B:ARG528 4.5 37.4 1.0
CE1 B:PHE222 4.6 36.4 1.0
CD B:ARG528 4.8 37.6 1.0
CZ B:PHE222 4.8 36.0 1.0
CB B:VAL409 4.8 42.2 1.0
OG B:SER527 4.9 37.9 1.0
O B:SER527 4.9 36.8 1.0
OE2 B:GLU410 5.0 46.9 1.0
C B:SER527 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in 6yua

Go back to Magnesium Binding Sites List in 6yua
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
C:Mg705

b:29.4
occ:1.00
 OE1 C:GLU495 3.1 64.2 1.0
CB C:GLN493 3.4 50.8 1.0
CG C:GLN493 3.5 52.0 1.0
OE2 C:GLU495 3.7 66.2 1.0
CD C:GLU495 3.8 64.8 1.0
CD C:GLN493 3.9 54.0 1.0
CA C:GLN493 4.0 50.0 1.0
CD1 C:ILE404 4.1 52.2 1.0
OE1 C:GLN493 4.2 54.3 1.0
CG1 C:ILE404 4.3 51.4 1.0
CB C:LYS402 4.4 60.2 1.0
N C:LYS494 4.4 51.6 1.0
NE2 C:GLN493 4.5 55.9 1.0
C C:GLN493 4.7 50.8 1.0
CD C:LYS402 4.8 65.0 1.0

Magnesium binding site 4 out of 4 in 6yua

Go back to Magnesium Binding Sites List in 6yua
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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
C:Mg706

b:12.2
occ:1.00
 OE1 C:GLU131 3.4 78.9 1.0
O C:ASN129 3.6 75.8 1.0
C C:ASN129 3.8 74.4 1.0
CA C:ASN129 4.1 74.1 1.0
CB C:ASN129 4.2 78.0 1.0
OD1 C:ASN129 4.3 84.0 1.0
CD C:GLU131 4.3 79.2 1.0
CG C:GLU131 4.5 79.1 1.0
N C:VAL130 4.5 73.1 1.0
CG C:ASN129 4.7 80.3 1.0
N C:GLU131 4.9 75.9 1.0
C C:VAL130 4.9 74.6 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: Wed Oct 2 01:08:36 2024

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