Magnesium in PDB 8p5x: Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi

Enzymatic activity of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi

All present enzymatic activity of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi:
1.2.4.2; 2.3.1.61;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi (pdb code 8p5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi, PDB code: 8p5x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p5x

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Magnesium binding site 1 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:54.6
occ:1.00
 OD1 A:ASN678 2.3 55.3 1.0
O2A A:TPP1301 2.4 90.0 1.0
O A:ILE680 2.5 96.6 1.0
O3B A:TPP1301 2.9 81.9 1.0
OD2 A:ASP645 3.2 53.8 1.0
OD1 A:ASP645 3.2 57.4 1.0
O3A A:TPP1301 3.2 87.0 1.0
CG A:ASN678 3.3 46.3 1.0
CG A:ASP645 3.3 50.6 1.0
PB A:TPP1301 3.4 74.3 1.0
PA A:TPP1301 3.4 85.1 1.0
C A:ILE680 3.7 92.8 1.0
O1B A:TPP1301 3.7 80.4 1.0
ND2 A:ASN678 3.8 53.6 1.0
N A:ASP645 4.1 28.5 1.0
O A:VAL676 4.4 37.7 1.0
N A:ILE680 4.4 71.3 1.0
N A:ASN678 4.4 36.3 1.0
O7 A:TPP1301 4.4 104.0 1.0
N A:GLY681 4.4 103.8 1.0
CA A:GLY681 4.5 112.6 1.0
CB A:ASP645 4.5 40.0 1.0
O1A A:TPP1301 4.5 89.4 1.0
CB A:ASN678 4.6 43.2 1.0
O A:GLY681 4.6 126.6 1.0
N A:ALA646 4.6 30.3 1.0
CA A:ILE680 4.7 81.9 1.0
CA A:ASP645 4.8 30.5 1.0
N A:GLN679 4.8 45.0 1.0
CA A:ASN678 4.8 38.5 1.0
C A:ASN678 4.9 40.1 1.0
O2B A:TPP1301 4.9 81.9 1.0
C A:GLY644 4.9 26.0 1.0
CA A:GLY644 5.0 24.9 1.0

Magnesium binding site 2 out of 6 in 8p5x

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Magnesium binding site 2 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:51.2
occ:1.00
 OD1 B:ASN678 2.3 57.4 1.0
O1A B:TPP1301 2.4 85.4 1.0
O B:ILE680 2.5 112.7 1.0
O1B B:TPP1301 2.9 79.0 1.0
O3A B:TPP1301 3.1 83.4 1.0
OD2 B:ASP645 3.2 56.0 1.0
CG B:ASN678 3.3 48.4 1.0
OD1 B:ASP645 3.3 58.7 1.0
PB B:TPP1301 3.3 70.8 1.0
CG B:ASP645 3.4 52.3 1.0
PA B:TPP1301 3.4 79.6 1.0
O3B B:TPP1301 3.6 76.7 1.0
ND2 B:ASN678 3.7 55.8 1.0
C B:ILE680 3.7 111.5 1.0
N B:ASP645 4.1 29.4 1.0
O B:VAL676 4.3 36.5 1.0
N B:ASN678 4.4 36.6 1.0
O7 B:TPP1301 4.4 101.3 1.0
N B:ILE680 4.4 84.3 1.0
N B:GLY681 4.5 128.2 1.0
O2A B:TPP1301 4.5 83.9 1.0
CA B:GLY681 4.5 140.2 1.0
CB B:ASP645 4.5 40.3 1.0
CB B:ASN678 4.5 44.5 1.0
O B:GLY681 4.6 152.9 1.0
N B:ALA646 4.7 30.3 1.0
CA B:ILE680 4.7 98.2 1.0
CA B:ASN678 4.8 40.1 1.0
N B:GLN679 4.8 50.1 1.0
CA B:ASP645 4.8 30.7 1.0
O2B B:TPP1301 4.8 78.7 1.0
C B:ASN678 4.8 44.1 1.0
C B:GLY644 4.9 26.5 1.0
CA B:GLY644 5.0 24.8 1.0

Magnesium binding site 3 out of 6 in 8p5x

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Magnesium binding site 3 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:53.9
occ:1.00
 OD1 C:ASN678 2.3 55.7 1.0
O2A C:TPP1302 2.4 88.7 1.0
O C:ILE680 2.5 98.5 1.0
O3B C:TPP1302 2.9 81.2 1.0
OD2 C:ASP645 3.2 54.2 1.0
OD1 C:ASP645 3.2 57.8 1.0
O3A C:TPP1302 3.3 85.7 1.0
CG C:ASN678 3.3 47.0 1.0
CG C:ASP645 3.3 51.1 1.0
PB C:TPP1302 3.4 73.1 1.0
PA C:TPP1302 3.4 83.8 1.0
C C:ILE680 3.7 94.4 1.0
O1B C:TPP1302 3.7 79.5 1.0
ND2 C:ASN678 3.8 54.4 1.0
N C:ASP645 4.1 28.9 1.0
O C:VAL676 4.3 38.1 1.0
N C:ILE680 4.4 72.4 1.0
N C:ASN678 4.4 36.7 1.0
O7 C:TPP1302 4.4 101.2 1.0
N C:GLY681 4.5 105.5 1.0
CA C:GLY681 4.5 114.3 1.0
CB C:ASP645 4.5 40.4 1.0
O1A C:TPP1302 4.5 88.5 1.0
CB C:ASN678 4.6 43.9 1.0
N C:ALA646 4.6 30.5 1.0
O C:GLY681 4.6 128.1 1.0
CA C:ILE680 4.7 83.0 1.0
CA C:ASP645 4.8 30.7 1.0
N C:GLN679 4.8 45.6 1.0
CA C:ASN678 4.8 39.0 1.0
C C:ASN678 4.9 40.6 1.0
O2B C:TPP1302 4.9 81.1 1.0
C C:GLY644 4.9 26.4 1.0
CA C:GLY644 5.0 25.3 1.0

Magnesium binding site 4 out of 6 in 8p5x

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Magnesium binding site 4 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1302

b:50.5
occ:1.00
 OD1 D:ASN678 2.3 57.7 1.0
O1A D:TPP1301 2.4 85.8 1.0
O D:ILE680 2.5 114.2 1.0
O1B D:TPP1301 2.9 79.9 1.0
O3A D:TPP1301 3.2 83.8 1.0
OD2 D:ASP645 3.2 55.7 1.0
CG D:ASN678 3.3 48.7 1.0
OD1 D:ASP645 3.3 58.5 1.0
PB D:TPP1301 3.3 71.2 1.0
CG D:ASP645 3.4 52.1 1.0
PA D:TPP1301 3.4 79.9 1.0
O3B D:TPP1301 3.6 77.4 1.0
ND2 D:ASN678 3.7 56.2 1.0
C D:ILE680 3.7 112.9 1.0
N D:ASP645 4.1 29.3 1.0
O D:VAL676 4.3 36.8 1.0
N D:ASN678 4.3 36.7 1.0
O7 D:TPP1301 4.4 101.8 1.0
N D:ILE680 4.4 85.5 1.0
O2A D:TPP1301 4.5 84.8 1.0
N D:GLY681 4.5 129.5 1.0
CB D:ASP645 4.5 40.1 1.0
CA D:GLY681 4.5 141.8 1.0
CB D:ASN678 4.5 44.7 1.0
O D:GLY681 4.6 154.6 1.0
N D:ALA646 4.7 30.0 1.0
CA D:ILE680 4.7 99.5 1.0
CA D:ASN678 4.8 40.2 1.0
CA D:ASP645 4.8 30.5 1.0
N D:GLN679 4.8 50.5 1.0
O2B D:TPP1301 4.8 78.9 1.0
C D:ASN678 4.8 44.4 1.0
C D:GLY644 4.9 26.4 1.0
CA D:GLY644 4.9 24.7 1.0

Magnesium binding site 5 out of 6 in 8p5x

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Magnesium binding site 5 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1302

b:53.5
occ:1.00
 OD1 E:ASN678 2.3 55.4 1.0
O2A E:TPP1301 2.4 89.2 1.0
O E:ILE680 2.5 97.2 1.0
O3B E:TPP1301 2.9 81.4 1.0
OD2 E:ASP645 3.2 53.8 1.0
O3A E:TPP1301 3.2 85.3 1.0
OD1 E:ASP645 3.2 57.4 1.0
CG E:ASN678 3.3 46.6 1.0
CG E:ASP645 3.3 50.7 1.0
PA E:TPP1301 3.4 83.9 1.0
PB E:TPP1301 3.4 73.0 1.0
C E:ILE680 3.7 93.6 1.0
O1B E:TPP1301 3.7 79.5 1.0
ND2 E:ASN678 3.8 53.9 1.0
N E:ASP645 4.1 28.5 1.0
O E:VAL676 4.4 38.1 1.0
O7 E:TPP1301 4.4 101.9 1.0
N E:ILE680 4.4 71.8 1.0
N E:ASN678 4.4 36.2 1.0
N E:GLY681 4.5 105.0 1.0
CA E:GLY681 4.5 114.2 1.0
CB E:ASP645 4.5 39.9 1.0
O1A E:TPP1301 4.5 88.4 1.0
CB E:ASN678 4.6 43.4 1.0
N E:ALA646 4.6 30.0 1.0
O E:GLY681 4.6 128.2 1.0
CA E:ILE680 4.7 82.8 1.0
CA E:ASP645 4.8 30.3 1.0
N E:GLN679 4.8 45.1 1.0
CA E:ASN678 4.8 38.5 1.0
C E:ASN678 4.9 40.3 1.0
O2B E:TPP1301 4.9 80.8 1.0
C E:GLY644 4.9 26.1 1.0
CA E:GLY644 5.0 25.1 1.0

Magnesium binding site 6 out of 6 in 8p5x

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Magnesium binding site 6 out of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1302

b:40.8
occ:1.00
 OD1 F:ASN678 2.3 58.0 1.0
O1A F:TPP1301 2.4 78.2 1.0
O F:ILE680 2.4 100.6 1.0
O1B F:TPP1301 2.9 73.0 1.0
O3A F:TPP1301 3.2 76.0 1.0
OD2 F:ASP645 3.2 56.1 1.0
OD1 F:ASP645 3.3 58.8 1.0
CG F:ASN678 3.3 49.6 1.0
PA F:TPP1301 3.4 71.2 1.0
CG F:ASP645 3.4 53.1 1.0
PB F:TPP1301 3.4 63.5 1.0
C F:ILE680 3.6 97.6 1.0
ND2 F:ASN678 3.7 57.8 1.0
O3B F:TPP1301 3.7 69.7 1.0
N F:ASP645 4.1 29.1 1.0
O7 F:TPP1301 4.3 91.7 1.0
N F:ILE680 4.4 75.3 1.0
O F:VAL676 4.4 34.1 1.0
N F:GLY681 4.4 111.3 1.0
N F:ASN678 4.4 36.6 1.0
CA F:GLY681 4.4 122.0 1.0
O2A F:TPP1301 4.5 76.0 1.0
CB F:ASP645 4.6 41.7 1.0
O F:GLY681 4.6 136.6 1.0
CB F:ASN678 4.6 44.5 1.0
CA F:ILE680 4.6 85.7 1.0
N F:ALA646 4.7 32.3 1.0
N F:GLN679 4.8 48.0 1.0
CA F:ASN678 4.8 40.1 1.0
CA F:ASP645 4.8 32.0 1.0
C F:ASN678 4.9 43.2 1.0
O2B F:TPP1301 4.9 71.7 1.0
C F:GLY644 5.0 26.1 1.0
CG2 F:ILE680 5.0 91.5 1.0

Reference:

L.Yang, T.Wagner, A.Mechaly, A.Boyko, E.M.Bruch, D.Megrian, F.Gubellini, P.M.Alzari, M.Bellinzoni. High Resolution Cryo-Em and Crystallographic Snapshots of the Actinobacterial Two-in-One 2-Oxoglutarate Dehydrogenase Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-40253-6
Page generated: Fri Oct 4 15:55:57 2024

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