Magnesium in PDB 9ev6: Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct

Protein crystallography data

The structure of Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct, PDB code: 9ev6 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) 37.46 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.554, 98.481, 110.515, 90, 90.84, 90
R / Rfree (%) 16.8 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct (pdb code 9ev6). 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 Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct, PDB code: 9ev6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9ev6

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Magnesium binding site 1 out of 4 in the Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:27.8
occ:1.00
 OD1 A:ASP436 1.9 30.6 1.0
O2A A:TPP702 2.0 31.6 1.0
O A:HOH836 2.1 23.2 1.0
O A:SER465 2.1 34.2 1.0
OD1 A:ASN463 2.1 38.4 1.0
O3B A:TPP702 2.1 32.0 1.0
CG A:ASP436 3.1 32.9 1.0
CG A:ASN463 3.1 37.6 1.0
PA A:TPP702 3.2 32.3 1.0
PB A:TPP702 3.2 32.6 1.0
C A:SER465 3.3 34.9 1.0
O3A A:TPP702 3.4 32.4 1.0
ND2 A:ASN463 3.4 36.9 1.0
OD2 A:ASP436 3.7 34.5 1.0
O1B A:TPP702 3.8 33.3 1.0
N A:SER465 3.9 37.0 1.0
N A:ASP436 3.9 29.2 1.0
O7 A:TPP702 3.9 33.8 1.0
N A:GLY467 4.1 35.2 1.0
CA A:SER465 4.1 37.3 1.0
N A:GLY437 4.1 29.0 1.0
CB A:ASP436 4.3 30.6 1.0
N A:LEU466 4.3 34.1 1.0
O A:PHE461 4.3 33.5 1.0
O1A A:TPP702 4.4 32.1 1.0
O A:HOH873 4.4 48.7 1.0
N A:ASN463 4.4 33.0 1.0
CB A:ASN463 4.5 34.9 1.0
O2B A:TPP702 4.5 32.4 1.0
CA A:LEU466 4.5 34.6 1.0
CA A:ASP436 4.5 29.5 1.0
CB A:SER465 4.7 40.5 1.0
N A:SER464 4.8 35.8 1.0
C A:GLY435 4.8 29.4 1.0
CA A:ASN463 4.8 34.5 1.0
CA A:GLY435 4.8 29.4 1.0
C A:ASN463 4.8 35.6 1.0
C A:ASP436 4.9 29.8 1.0
C A:LEU466 4.9 35.4 1.0
CA A:GLY467 4.9 36.7 1.0

Magnesium binding site 2 out of 4 in 9ev6

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Magnesium binding site 2 out of 4 in the Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:28.0
occ:1.00
 OD1 B:ASP436 2.0 33.6 1.0
O1B B:TPP702 2.0 30.7 1.0
O B:HOH832 2.0 25.6 1.0
OD1 B:ASN463 2.0 31.1 1.0
O2A B:TPP702 2.1 29.3 1.0
O B:SER465 2.2 33.2 1.0
CG B:ASN463 3.0 32.4 1.0
PB B:TPP702 3.1 29.9 1.0
CG B:ASP436 3.1 32.8 1.0
PA B:TPP702 3.2 29.7 1.0
O3A B:TPP702 3.3 29.3 1.0
ND2 B:ASN463 3.4 32.4 1.0
C B:SER465 3.4 33.4 1.0
O3B B:TPP702 3.7 30.4 1.0
OD2 B:ASP436 3.7 35.4 1.0
N B:ASP436 3.9 28.7 1.0
O7 B:TPP702 4.0 31.1 1.0
N B:SER465 4.0 35.0 1.0
O B:PHE461 4.2 33.2 1.0
N B:GLY467 4.2 32.0 1.0
N B:GLY437 4.2 27.4 1.0
CA B:SER465 4.2 35.4 1.0
CB B:ASP436 4.3 29.2 1.0
N B:ASN463 4.4 33.2 1.0
N B:LEU466 4.4 32.6 1.0
CB B:ASN463 4.4 30.9 1.0
O2B B:TPP702 4.4 29.0 1.0
O1A B:TPP702 4.4 30.0 1.0
CA B:ASP436 4.5 27.8 1.0
CA B:LEU466 4.6 32.4 1.0
O B:HOH942 4.6 32.9 1.0
C B:GLY435 4.7 30.0 1.0
CA B:GLY435 4.7 31.0 1.0
CB B:SER465 4.8 36.8 1.0
CA B:ASN463 4.8 32.8 1.0
N B:SER464 4.8 34.1 1.0
C B:ASN463 4.9 33.6 1.0
C B:ASP436 4.9 27.3 1.0
C B:LEU466 4.9 32.5 1.0
CA B:GLY467 5.0 31.7 1.0

Magnesium binding site 3 out of 4 in 9ev6

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Magnesium binding site 3 out of 4 in the Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:30.9
occ:1.00
 OD1 C:ASP436 1.9 35.5 1.0
O2A C:TPP702 2.0 28.6 1.0
O C:SER465 2.0 31.2 1.0
OD1 C:ASN463 2.1 31.4 1.0
O3B C:TPP702 2.1 30.7 1.0
O C:HOH855 2.2 25.3 1.0
CG C:ASP436 3.1 34.9 1.0
CG C:ASN463 3.1 31.2 1.0
PA C:TPP702 3.2 29.7 1.0
PB C:TPP702 3.2 30.6 1.0
C C:SER465 3.3 32.0 1.0
O3A C:TPP702 3.4 29.9 1.0
ND2 C:ASN463 3.5 29.9 1.0
OD2 C:ASP436 3.6 35.9 1.0
O1B C:TPP702 3.8 30.1 1.0
N C:SER465 3.9 34.5 1.0
N C:ASP436 3.9 30.8 1.0
O7 C:TPP702 3.9 30.3 1.0
CA C:SER465 4.1 33.9 1.0
N C:GLY467 4.1 30.2 1.0
N C:GLY437 4.1 29.4 1.0
N C:LEU466 4.3 30.8 1.0
CB C:ASP436 4.3 32.4 1.0
O C:HOH933 4.3 33.5 1.0
O C:PHE461 4.3 33.5 1.0
O1A C:TPP702 4.4 28.9 1.0
CA C:LEU466 4.5 29.9 1.0
CB C:ASN463 4.5 31.3 1.0
N C:ASN463 4.5 31.5 1.0
O2B C:TPP702 4.5 31.1 1.0
CA C:ASP436 4.5 30.9 1.0
CB C:SER465 4.7 35.2 1.0
C C:GLY435 4.8 31.6 1.0
N C:SER464 4.8 33.2 1.0
CA C:GLY435 4.8 31.9 1.0
C C:ASN463 4.8 33.2 1.0
CA C:ASN463 4.8 31.8 1.0
C C:ASP436 4.8 30.3 1.0
C C:LEU466 4.9 30.1 1.0
CA C:GLY467 5.0 31.2 1.0

Magnesium binding site 4 out of 4 in 9ev6

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Magnesium binding site 4 out of 4 in the Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Corynebacterium Glutamicum Pyruvate:Quinone Oxidoreductase (Pqo), C- Terminal Truncated Construct within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:49.4
occ:1.00
 OD1 D:ASP436 2.0 45.0 1.0
O2A D:TPP702 2.0 44.1 1.0
O3B D:TPP702 2.0 44.0 1.0
O D:HOH832 2.1 34.2 1.0
OD1 D:ASN463 2.1 49.8 1.0
O D:SER465 2.1 48.9 1.0
CG D:ASN463 3.1 49.4 1.0
CG D:ASP436 3.1 45.9 1.0
PB D:TPP702 3.2 44.6 1.0
PA D:TPP702 3.2 43.8 1.0
O3A D:TPP702 3.3 44.1 1.0
C D:SER465 3.3 49.3 1.0
ND2 D:ASN463 3.4 48.5 1.0
OD2 D:ASP436 3.7 48.6 1.0
O1B D:TPP702 3.7 43.9 1.0
O7 D:TPP702 3.9 43.9 1.0
N D:ASP436 3.9 40.4 1.0
N D:SER465 3.9 49.8 1.0
N D:GLY467 4.1 49.8 1.0
CA D:SER465 4.2 50.2 1.0
N D:GLY437 4.2 38.5 1.0
CB D:ASP436 4.3 42.3 1.0
O D:PHE461 4.3 46.2 1.0
N D:LEU466 4.3 48.7 1.0
O1A D:TPP702 4.4 43.5 1.0
N D:ASN463 4.4 46.3 1.0
O2B D:TPP702 4.4 44.0 1.0
CB D:ASN463 4.4 47.6 1.0
CA D:LEU466 4.5 49.1 1.0
CA D:ASP436 4.5 40.2 1.0
CB D:SER465 4.7 52.7 1.0
C D:GLY435 4.8 41.6 1.0
CA D:ASN463 4.8 47.1 1.0
CA D:GLY435 4.8 42.3 1.0
C D:ASN463 4.8 48.0 1.0
N D:SER464 4.8 47.7 1.0
C D:ASP436 4.9 39.7 1.0
C D:LEU466 4.9 49.4 1.0
CA D:GLY467 4.9 51.0 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 08:59:00 2024

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