Magnesium in PDB 9ev5: Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion

Enzymatic activity of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion

All present enzymatic activity of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion:
1.2.5.1;

Protein crystallography data

The structure of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion, PDB code: 9ev5 was solved by C.Da Silva Lameira, S.Muenssinger, L.Yang, B.J.Eikmanns, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 155.33 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.192, 77.935, 158.044, 90, 100.63, 90
R / Rfree (%) 20.7 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion (pdb code 9ev5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion, PDB code: 9ev5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9ev5

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Magnesium binding site 1 out of 4 in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:24.9
occ:1.00
 O2B A:TPP601 2.1 16.2 1.0
OD1 A:ASP436 2.1 22.1 1.0
OD1 A:ASN463 2.1 23.5 1.0
O2A A:TPP601 2.2 17.3 1.0
O A:SER465 2.3 19.2 1.0
CG A:ASN463 3.0 22.1 1.0
PB A:TPP601 3.1 17.3 1.0
PA A:TPP601 3.2 18.4 1.0
O3A A:TPP601 3.2 18.5 1.0
ND2 A:ASN463 3.2 19.5 1.0
CG A:ASP436 3.3 22.9 1.0
O1B A:TPP601 3.5 17.2 1.0
C A:SER465 3.5 20.0 1.0
N A:ASP436 3.8 16.4 1.0
OD2 A:ASP436 3.9 26.4 1.0
O7 A:TPP601 4.0 18.5 1.0
N A:GLY467 4.1 19.4 1.0
O A:PHE461 4.1 18.8 1.0
N A:SER465 4.2 22.0 1.0
N A:GLY437 4.3 16.0 1.0
CB A:ASN463 4.4 19.4 1.0
CB A:ASP436 4.4 18.9 1.0
O3B A:TPP601 4.4 18.5 1.0
N A:ASN463 4.4 18.3 1.0
CA A:SER465 4.4 21.0 1.0
O1A A:TPP601 4.5 18.9 1.0
N A:LEU466 4.5 19.4 1.0
CA A:GLY435 4.6 18.0 1.0
CA A:ASP436 4.6 16.9 1.0
C A:GLY435 4.6 17.3 1.0
CA A:LEU466 4.6 19.3 1.0
CA A:GLY467 4.8 20.1 1.0
CA A:ASN463 4.8 19.3 1.0
C A:LEU466 4.9 19.4 1.0
CB A:SER465 4.9 23.4 1.0
N A:SER464 5.0 20.9 1.0
O A:HOH952 5.0 26.4 1.0
C A:ASP436 5.0 17.0 1.0

Magnesium binding site 2 out of 4 in 9ev5

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Magnesium binding site 2 out of 4 in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:18.1
occ:1.00
 O B:HOH734 2.1 9.2 1.0
O2B B:TPP601 2.1 19.9 1.0
OD1 B:ASP436 2.1 18.3 1.0
OD1 B:ASN463 2.1 22.9 1.0
O2A B:TPP601 2.2 19.6 1.0
O B:SER465 2.2 16.3 1.0
CG B:ASN463 3.0 21.8 1.0
PB B:TPP601 3.1 18.8 1.0
PA B:TPP601 3.2 18.7 1.0
CG B:ASP436 3.2 19.4 1.0
ND2 B:ASN463 3.2 20.8 1.0
O3A B:TPP601 3.3 19.2 1.0
C B:SER465 3.4 18.0 1.0
O1B B:TPP601 3.6 17.6 1.0
OD2 B:ASP436 3.8 21.3 1.0
N B:ASP436 3.9 17.4 1.0
O7 B:TPP601 4.0 17.3 1.0
N B:GLY467 4.0 21.1 1.0
N B:SER465 4.1 20.4 1.0
O B:PHE461 4.2 18.4 1.0
N B:GLY437 4.3 17.5 1.0
CA B:SER465 4.3 20.0 1.0
CB B:ASP436 4.4 17.9 1.0
N B:LEU466 4.4 18.4 1.0
CB B:ASN463 4.4 19.3 1.0
O3B B:TPP601 4.4 20.1 1.0
N B:ASN463 4.4 20.6 1.0
O1A B:TPP601 4.5 18.6 1.0
CA B:LEU466 4.6 18.9 1.0
CA B:ASP436 4.6 17.1 1.0
CA B:GLY435 4.7 19.3 1.0
C B:GLY435 4.7 18.1 1.0
CA B:GLY467 4.8 22.4 1.0
CA B:ASN463 4.8 20.1 1.0
CB B:SER465 4.8 21.7 1.0
C B:LEU466 4.9 19.7 1.0
N B:SER464 4.9 20.0 1.0
C B:ASP436 5.0 17.8 1.0
C B:ASN463 5.0 19.8 1.0

Magnesium binding site 3 out of 4 in 9ev5

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Magnesium binding site 3 out of 4 in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:29.4
occ:1.00
 O C:HOH822 1.9 19.2 1.0
OD1 C:ASP436 2.0 43.3 1.0
O2B C:TPP601 2.1 34.5 1.0
O2A C:TPP601 2.1 33.6 1.0
OD1 C:ASN463 2.1 42.3 1.0
O C:SER465 2.2 38.9 1.0
CG C:ASN463 3.1 42.0 1.0
PB C:TPP601 3.1 33.7 1.0
CG C:ASP436 3.2 43.1 1.0
PA C:TPP601 3.2 32.5 1.0
O3A C:TPP601 3.3 33.1 1.0
ND2 C:ASN463 3.3 42.0 1.0
C C:SER465 3.4 39.4 1.0
O1B C:TPP601 3.6 32.7 1.0
OD2 C:ASP436 3.8 45.1 1.0
N C:ASP436 3.8 37.6 1.0
O7 C:TPP601 4.0 32.2 1.0
N C:GLY467 4.1 38.9 1.0
N C:SER465 4.1 40.7 1.0
O C:PHE461 4.2 42.0 1.0
N C:GLY437 4.3 35.0 1.0
CA C:SER465 4.3 40.1 1.0
CB C:ASP436 4.3 39.3 1.0
N C:LEU466 4.4 38.8 1.0
CB C:ASN463 4.4 41.3 1.0
N C:ASN463 4.4 42.0 1.0
O1A C:TPP601 4.5 31.6 1.0
O3B C:TPP601 4.5 34.2 1.0
CA C:ASP436 4.5 37.3 1.0
CA C:LEU466 4.6 38.8 1.0
CA C:GLY435 4.7 39.2 1.0
C C:GLY435 4.7 38.8 1.0
O C:HOH768 4.7 35.3 1.0
CA C:ASN463 4.8 42.0 1.0
CB C:SER465 4.8 40.4 1.0
CA C:GLY467 4.8 39.4 1.0
N C:SER464 4.9 42.1 1.0
C C:LEU466 4.9 38.8 1.0
C C:ASP436 4.9 36.4 1.0
C C:ASN463 5.0 42.8 1.0

Magnesium binding site 4 out of 4 in 9ev5

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Magnesium binding site 4 out of 4 in the Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Corynebacterium Glutamicum CS176 Pyruvate:Quinone Oxidoreductase (Pqo) in Complex with Fad and Thiamine Diphosphate-Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:50.3
occ:1.00
 OD1 D:ASP436 2.0 48.5 1.0
O2B D:TPP601 2.1 37.2 1.0
OD1 D:ASN463 2.2 52.2 1.0
O2A D:TPP601 2.2 37.2 1.0
O D:SER465 2.3 44.1 1.0
CG D:ASN463 3.0 51.4 1.0
PB D:TPP601 3.1 37.6 1.0
CG D:ASP436 3.2 49.0 1.0
ND2 D:ASN463 3.3 51.3 1.0
PA D:TPP601 3.3 36.4 1.0
O3A D:TPP601 3.3 36.9 1.0
C D:SER465 3.5 44.8 1.0
O1B D:TPP601 3.5 37.2 1.0
N D:ASP436 3.8 44.0 1.0
OD2 D:ASP436 3.9 51.4 1.0
O7 D:TPP601 4.0 35.9 1.0
N D:GLY467 4.1 45.9 1.0
O D:PHE461 4.1 47.8 1.0
N D:SER465 4.2 46.6 1.0
N D:GLY437 4.3 42.9 1.0
CB D:ASP436 4.3 45.7 1.0
CA D:SER465 4.4 45.7 1.0
CB D:ASN463 4.4 50.5 1.0
O3B D:TPP601 4.4 37.4 1.0
N D:ASN463 4.4 50.0 1.0
N D:LEU466 4.5 44.0 1.0
O1A D:TPP601 4.5 36.3 1.0
CA D:ASP436 4.6 43.9 1.0
CA D:GLY435 4.6 45.2 1.0
CA D:LEU466 4.6 44.4 1.0
C D:GLY435 4.7 45.0 1.0
O D:HOH840 4.8 45.9 1.0
CA D:ASN463 4.8 50.5 1.0
CA D:GLY467 4.9 46.9 1.0
CB D:SER465 4.9 47.5 1.0
N D:SER464 4.9 50.0 1.0
C D:LEU466 4.9 44.8 1.0
C D:ASP436 5.0 44.0 1.0
C D:ASN463 5.0 51.4 1.0

Reference:

C.Da Silva Lameira, S.Munssinger, L.Yang, B.J.Eikmanns, M.Bellinzoni. Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase: An Enigmatic Metabolic Enzyme with Unusual Structural Features. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 39080980
DOI: 10.1111/FEBS.17232
Page generated: Sat Oct 5 08:59:01 2024

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