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Magnesium in PDB 8p5v: Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa

Enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa

All present enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa:
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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa (pdb code 8p5v). 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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa, PDB code: 8p5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p5v

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Magnesium binding site 1 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:38.0
occ:1.00
 OD1 A:ASN678 2.0 50.1 1.0
O A:ILE680 2.0 54.3 1.0
O1B A:TPP1303 2.1 49.7 1.0
OD1 A:ASP645 2.2 52.1 1.0
O1A A:TPP1303 2.2 50.5 1.0
CG A:ASN678 3.0 40.5 1.0
C A:ILE680 3.2 51.4 1.0
CG A:ASP645 3.2 48.5 1.0
PB A:TPP1303 3.3 46.0 1.0
PA A:TPP1303 3.3 48.8 1.0
ND2 A:ASN678 3.4 40.6 1.0
O3A A:TPP1303 3.4 51.2 1.0
OD2 A:ASP645 3.7 57.1 1.0
O2B A:TPP1303 3.9 51.0 1.0
N A:ILE680 4.0 49.0 1.0
O7 A:TPP1303 4.1 55.4 1.0
N A:GLY681 4.1 55.7 1.0
N A:ASP645 4.1 39.9 1.0
CA A:GLY681 4.2 58.9 1.0
CA A:ILE680 4.2 51.3 1.0
N A:ASN678 4.4 42.0 1.0
O A:VAL676 4.4 44.1 1.0
CB A:ASN678 4.4 41.7 1.0
N A:ALA646 4.4 43.2 1.0
CB A:ASP645 4.5 46.4 1.0
O2A A:TPP1303 4.5 52.2 1.0
O3B A:TPP1303 4.6 50.8 1.0
N A:GLN679 4.6 45.3 1.0
CG2 A:ILE680 4.6 52.9 1.0
CA A:ASN678 4.7 42.4 1.0
C A:ASN678 4.7 44.0 1.0
O A:GLY681 4.8 83.1 1.0
CA A:ASP645 4.8 42.7 1.0
CB A:ALA646 4.9 46.1 1.0
CA A:GLY644 4.9 37.5 1.0
C A:GLY644 4.9 38.4 1.0
C A:GLY681 5.0 69.5 1.0

Magnesium binding site 2 out of 6 in 8p5v

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Magnesium binding site 2 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:41.4
occ:1.00
 OD1 B:ASN678 2.0 52.3 1.0
O B:ILE680 2.0 60.2 1.0
O2A B:TPP1303 2.1 54.7 1.0
OD1 B:ASP645 2.2 55.2 1.0
O2B B:TPP1303 2.2 54.5 1.0
CG B:ASN678 3.0 43.5 1.0
PA B:TPP1303 3.2 51.7 1.0
C B:ILE680 3.3 57.6 1.0
CG B:ASP645 3.3 51.2 1.0
PB B:TPP1303 3.3 49.2 1.0
O3A B:TPP1303 3.4 53.3 1.0
ND2 B:ASN678 3.4 43.7 1.0
OD2 B:ASP645 3.7 60.9 1.0
O1B B:TPP1303 3.9 54.9 1.0
N B:ILE680 4.0 54.6 1.0
O7 B:TPP1303 4.1 59.7 1.0
N B:GLY681 4.1 61.3 1.0
N B:ASP645 4.1 44.4 1.0
CA B:GLY681 4.2 64.0 1.0
CA B:ILE680 4.2 56.1 1.0
N B:ASN678 4.4 44.5 1.0
CB B:ASN678 4.4 44.4 1.0
O B:VAL676 4.4 48.8 1.0
N B:ALA646 4.4 48.1 1.0
O1A B:TPP1303 4.4 53.4 1.0
CB B:ASP645 4.5 49.7 1.0
O3B B:TPP1303 4.6 55.0 1.0
CG2 B:ILE680 4.6 57.7 1.0
N B:GLN679 4.6 48.0 1.0
CA B:ASN678 4.7 44.6 1.0
C B:ASN678 4.7 46.4 1.0
O B:GLY681 4.8 86.5 1.0
CA B:ASP645 4.8 46.9 1.0
CB B:ALA646 4.9 50.6 1.0
CA B:GLY644 4.9 42.2 1.0
C B:GLY644 4.9 42.4 1.0
C B:GLY681 5.0 74.2 1.0

Magnesium binding site 3 out of 6 in 8p5v

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Magnesium binding site 3 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:39.2
occ:1.00
 OD1 C:ASN678 2.0 50.4 1.0
O C:ILE680 2.0 55.6 1.0
O1A C:TPP1303 2.1 49.8 1.0
O1B C:TPP1303 2.1 50.4 1.0
OD1 C:ASP645 2.2 51.5 1.0
CG C:ASN678 3.0 40.9 1.0
C C:ILE680 3.2 52.2 1.0
CG C:ASP645 3.3 48.7 1.0
PB C:TPP1303 3.3 46.2 1.0
PA C:TPP1303 3.3 48.0 1.0
ND2 C:ASN678 3.4 40.8 1.0
O3A C:TPP1303 3.4 50.9 1.0
OD2 C:ASP645 3.7 57.9 1.0
O2B C:TPP1303 3.9 51.5 1.0
N C:ILE680 4.0 49.5 1.0
O7 C:TPP1303 4.1 56.2 1.0
N C:GLY681 4.1 56.0 1.0
N C:ASP645 4.2 41.0 1.0
CA C:GLY681 4.2 59.3 1.0
CA C:ILE680 4.2 51.7 1.0
N C:ASN678 4.4 41.9 1.0
CB C:ASN678 4.4 41.8 1.0
O C:VAL676 4.4 44.9 1.0
N C:ALA646 4.5 44.0 1.0
O2A C:TPP1303 4.5 51.3 1.0
O3B C:TPP1303 4.6 51.5 1.0
CB C:ASP645 4.6 46.4 1.0
CG2 C:ILE680 4.6 53.6 1.0
N C:GLN679 4.6 45.3 1.0
CA C:ASN678 4.7 42.6 1.0
C C:ASN678 4.7 44.3 1.0
O C:GLY681 4.7 83.2 1.0
CA C:ASP645 4.8 43.3 1.0
CB C:ALA646 4.9 46.6 1.0
CA C:GLY644 4.9 39.6 1.0
C C:GLY644 5.0 39.7 1.0
C C:GLY681 5.0 69.9 1.0

Magnesium binding site 4 out of 6 in 8p5v

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Magnesium binding site 4 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1301

b:41.5
occ:1.00
 OD1 D:ASN678 2.0 52.1 1.0
O D:ILE680 2.0 60.7 1.0
O2A D:TPP1303 2.1 55.5 1.0
O2B D:TPP1303 2.2 54.8 1.0
OD1 D:ASP645 2.2 55.2 1.0
CG D:ASN678 3.0 43.2 1.0
PA D:TPP1303 3.2 52.2 1.0
C D:ILE680 3.2 57.9 1.0
PB D:TPP1303 3.3 49.3 1.0
CG D:ASP645 3.3 51.6 1.0
O3A D:TPP1303 3.4 53.5 1.0
ND2 D:ASN678 3.4 43.8 1.0
OD2 D:ASP645 3.7 61.1 1.0
O1B D:TPP1303 3.9 55.0 1.0
N D:ILE680 4.0 54.6 1.0
O7 D:TPP1303 4.1 60.0 1.0
N D:GLY681 4.1 62.2 1.0
N D:ASP645 4.1 44.2 1.0
CA D:GLY681 4.2 64.9 1.0
CA D:ILE680 4.2 56.5 1.0
N D:ASN678 4.4 44.5 1.0
CB D:ASN678 4.4 44.3 1.0
O D:VAL676 4.4 48.7 1.0
N D:ALA646 4.4 47.9 1.0
O1A D:TPP1303 4.4 53.7 1.0
CB D:ASP645 4.5 49.9 1.0
O3B D:TPP1303 4.5 54.8 1.0
CG2 D:ILE680 4.6 57.9 1.0
N D:GLN679 4.6 48.3 1.0
CA D:ASN678 4.7 44.6 1.0
C D:ASN678 4.7 46.4 1.0
O D:GLY681 4.8 86.8 1.0
CA D:ASP645 4.8 46.7 1.0
CB D:ALA646 4.9 50.4 1.0
CA D:GLY644 4.9 41.8 1.0
C D:GLY644 4.9 42.0 1.0
C D:GLY681 5.0 74.6 1.0

Magnesium binding site 5 out of 6 in 8p5v

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Magnesium binding site 5 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1301

b:38.7
occ:1.00
 OD1 E:ASN678 2.0 50.3 1.0
O E:ILE680 2.0 56.1 1.0
O1A E:TPP1303 2.1 49.6 1.0
O1B E:TPP1303 2.1 49.9 1.0
OD1 E:ASP645 2.2 52.7 1.0
CG E:ASN678 3.0 40.2 1.0
C E:ILE680 3.2 52.7 1.0
PB E:TPP1303 3.2 45.5 1.0
PA E:TPP1303 3.3 47.8 1.0
CG E:ASP645 3.3 50.3 1.0
ND2 E:ASN678 3.4 40.2 1.0
O3A E:TPP1303 3.4 50.2 1.0
OD2 E:ASP645 3.8 57.4 1.0
O2B E:TPP1303 3.8 51.2 1.0
N E:ILE680 4.0 49.9 1.0
O7 E:TPP1303 4.1 55.2 1.0
N E:GLY681 4.1 56.6 1.0
N E:ASP645 4.2 40.8 1.0
CA E:GLY681 4.2 59.7 1.0
CA E:ILE680 4.2 51.6 1.0
CB E:ASN678 4.4 41.6 1.0
O E:VAL676 4.4 44.4 1.0
N E:ASN678 4.4 41.4 1.0
N E:ALA646 4.5 44.4 1.0
O2A E:TPP1303 4.5 51.2 1.0
O3B E:TPP1303 4.5 51.7 1.0
CB E:ASP645 4.6 46.9 1.0
CG2 E:ILE680 4.6 53.6 1.0
N E:GLN679 4.6 45.1 1.0
O E:GLY681 4.7 84.0 1.0
CA E:ASN678 4.7 42.2 1.0
C E:ASN678 4.7 44.3 1.0
CA E:ASP645 4.8 43.3 1.0
CA E:GLY644 4.9 38.1 1.0
C E:GLY681 4.9 70.3 1.0
CB E:ALA646 5.0 46.4 1.0
C E:GLY644 5.0 38.7 1.0

Magnesium binding site 6 out of 6 in 8p5v

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Magnesium binding site 6 out of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1301

b:41.5
occ:1.00
 OD1 F:ASN678 2.0 52.0 1.0
O F:ILE680 2.0 60.6 1.0
O2A F:TPP1303 2.1 56.0 1.0
O2B F:TPP1303 2.1 55.1 1.0
OD1 F:ASP645 2.2 56.2 1.0
CG F:ASN678 3.0 43.5 1.0
PB F:TPP1303 3.3 50.0 1.0
PA F:TPP1303 3.3 52.6 1.0
C F:ILE680 3.3 58.0 1.0
CG F:ASP645 3.3 52.0 1.0
O3A F:TPP1303 3.4 54.4 1.0
ND2 F:ASN678 3.4 43.4 1.0
OD2 F:ASP645 3.7 61.5 1.0
O1B F:TPP1303 3.9 55.2 1.0
N F:ILE680 4.0 54.8 1.0
O7 F:TPP1303 4.1 60.7 1.0
N F:ASP645 4.1 44.9 1.0
N F:GLY681 4.1 62.0 1.0
CA F:GLY681 4.2 64.6 1.0
CA F:ILE680 4.2 56.4 1.0
N F:ASN678 4.4 44.3 1.0
O F:VAL676 4.4 48.9 1.0
CB F:ASN678 4.4 44.5 1.0
N F:ALA646 4.4 48.9 1.0
O1A F:TPP1303 4.4 54.4 1.0
O3B F:TPP1303 4.5 55.6 1.0
CB F:ASP645 4.5 50.4 1.0
N F:GLN679 4.6 47.9 1.0
CG2 F:ILE680 4.6 57.8 1.0
CA F:ASN678 4.7 44.4 1.0
C F:ASN678 4.7 46.5 1.0
O F:GLY681 4.8 87.0 1.0
CA F:ASP645 4.8 47.3 1.0
CB F:ALA646 4.9 51.1 1.0
CA F:GLY644 4.9 42.5 1.0
C F:GLY644 4.9 42.5 1.0
C F:GLY681 5.0 74.3 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 Aug 15 12:13:43 2025

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