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Magnesium in PDB 8p5t: Single Particle Cryo-Em Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum

Enzymatic activity of Single Particle Cryo-Em Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum

All present enzymatic activity of Single Particle Cryo-Em Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum:
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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum (pdb code 8p5t). 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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum, PDB code: 8p5t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:19.8
occ:1.00
 O2B A:TPP1303 2.1 28.8 1.0
OD1 A:ASN678 2.2 37.9 1.0
O A:ILE680 2.3 34.3 1.0
O1A A:TPP1303 2.3 31.9 1.0
OD1 A:ASP645 2.4 54.2 1.0
CG A:ASP645 3.2 46.7 1.0
CG A:ASN678 3.2 26.0 1.0
OD2 A:ASP645 3.4 54.1 1.0
C A:ILE680 3.5 27.2 1.0
PB A:TPP1303 3.5 19.8 1.0
PA A:TPP1303 3.6 21.2 1.0
ND2 A:ASN678 3.7 28.8 1.0
O3A A:TPP1303 3.8 28.2 1.0
N A:ILE680 4.0 28.3 1.0
N A:ASP645 4.3 27.1 1.0
N A:ASN678 4.3 26.9 1.0
O3B A:TPP1303 4.3 29.6 1.0
CA A:ILE680 4.4 27.3 1.0
O A:VAL676 4.4 31.6 1.0
N A:GLY681 4.4 29.8 1.0
O1B A:TPP1303 4.5 28.4 1.0
CB A:ASN678 4.5 26.9 1.0
CB A:ASP645 4.5 37.3 1.0
CA A:GLY681 4.6 29.5 1.0
O7 A:TPP1303 4.6 29.1 1.0
N A:GLN679 4.6 27.4 1.0
C A:ASN678 4.6 27.2 1.0
O A:GLY681 4.7 52.2 1.0
CG2 A:ILE680 4.7 36.5 1.0
O2A A:TPP1303 4.7 30.7 1.0
CA A:ASN678 4.7 24.8 1.0
N A:ALA646 4.8 28.1 1.0
CA A:ASP645 4.9 28.3 1.0

Magnesium binding site 2 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:20.1
occ:1.00
 O2B B:TPP1303 2.1 29.1 1.0
OD1 B:ASN678 2.2 37.8 1.0
O B:ILE680 2.3 34.2 1.0
O2A B:TPP1303 2.3 32.1 1.0
OD1 B:ASP645 2.4 54.4 1.0
CG B:ASP645 3.2 46.8 1.0
CG B:ASN678 3.2 25.8 1.0
OD2 B:ASP645 3.5 54.2 1.0
C B:ILE680 3.5 27.1 1.0
PB B:TPP1303 3.5 19.9 1.0
PA B:TPP1303 3.6 21.4 1.0
ND2 B:ASN678 3.7 28.6 1.0
O3A B:TPP1303 3.8 28.4 1.0
N B:ILE680 4.0 28.3 1.0
N B:ASP645 4.3 27.0 1.0
O1B B:TPP1303 4.3 29.8 1.0
N B:ASN678 4.3 26.9 1.0
CA B:ILE680 4.4 27.3 1.0
O B:VAL676 4.4 31.8 1.0
N B:GLY681 4.4 29.7 1.0
CB B:ASN678 4.5 26.7 1.0
CB B:ASP645 4.5 37.4 1.0
O3B B:TPP1303 4.5 28.7 1.0
CA B:GLY681 4.6 29.3 1.0
O7 B:TPP1303 4.6 29.3 1.0
N B:GLN679 4.6 27.1 1.0
C B:ASN678 4.6 26.9 1.0
O1A B:TPP1303 4.7 31.0 1.0
O B:GLY681 4.7 52.3 1.0
CG2 B:ILE680 4.7 36.4 1.0
CA B:ASN678 4.7 24.6 1.0
N B:ALA646 4.8 28.1 1.0
CA B:ASP645 4.9 28.3 1.0

Magnesium binding site 3 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:19.5
occ:1.00
 O2B C:TPP1303 2.1 28.6 1.0
OD1 C:ASN678 2.2 37.7 1.0
O C:ILE680 2.3 34.1 1.0
O1A C:TPP1303 2.3 31.5 1.0
OD1 C:ASP645 2.4 54.4 1.0
CG C:ASP645 3.2 46.8 1.0
CG C:ASN678 3.2 25.8 1.0
OD2 C:ASP645 3.5 54.2 1.0
C C:ILE680 3.5 27.2 1.0
PB C:TPP1303 3.5 19.4 1.0
PA C:TPP1303 3.6 21.0 1.0
ND2 C:ASN678 3.7 28.4 1.0
O3A C:TPP1303 3.8 27.7 1.0
N C:ILE680 4.0 28.5 1.0
O3B C:TPP1303 4.3 29.5 1.0
N C:ASP645 4.3 27.0 1.0
N C:ASN678 4.3 26.6 1.0
CA C:ILE680 4.4 27.4 1.0
O C:VAL676 4.4 31.7 1.0
N C:GLY681 4.4 29.7 1.0
CB C:ASN678 4.5 26.7 1.0
CB C:ASP645 4.5 37.3 1.0
O1B C:TPP1303 4.5 27.8 1.0
CA C:GLY681 4.6 29.1 1.0
O7 C:TPP1303 4.6 28.7 1.0
N C:GLN679 4.6 27.4 1.0
C C:ASN678 4.6 27.2 1.0
O C:GLY681 4.7 52.0 1.0
CG2 C:ILE680 4.7 36.5 1.0
O2A C:TPP1303 4.7 30.6 1.0
CA C:ASN678 4.7 24.6 1.0
N C:ALA646 4.8 27.9 1.0
CA C:ASP645 4.9 28.2 1.0

Magnesium binding site 4 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1301

b:20.3
occ:1.00
 O2B D:TPP1303 2.1 29.2 1.0
OD1 D:ASN678 2.2 38.0 1.0
O D:ILE680 2.3 33.9 1.0
O2A D:TPP1303 2.3 32.0 1.0
OD1 D:ASP645 2.4 54.5 1.0
CG D:ASP645 3.2 46.9 1.0
CG D:ASN678 3.2 25.9 1.0
OD2 D:ASP645 3.5 54.3 1.0
C D:ILE680 3.5 26.9 1.0
PB D:TPP1303 3.5 19.6 1.0
PA D:TPP1303 3.6 21.3 1.0
ND2 D:ASN678 3.7 28.6 1.0
O3A D:TPP1303 3.8 28.0 1.0
N D:ILE680 4.1 28.2 1.0
O1B D:TPP1303 4.2 29.5 1.0
N D:ASP645 4.3 26.9 1.0
N D:ASN678 4.3 26.7 1.0
CA D:ILE680 4.4 27.3 1.0
O D:VAL676 4.4 32.1 1.0
N D:GLY681 4.4 29.5 1.0
CB D:ASN678 4.5 26.8 1.0
CB D:ASP645 4.5 37.3 1.0
O3B D:TPP1303 4.6 28.0 1.0
CA D:GLY681 4.6 29.1 1.0
O7 D:TPP1303 4.6 29.1 1.0
N D:GLN679 4.6 27.1 1.0
C D:ASN678 4.6 27.0 1.0
O D:GLY681 4.7 51.9 1.0
O1A D:TPP1303 4.7 31.0 1.0
CG2 D:ILE680 4.7 36.5 1.0
CA D:ASN678 4.7 24.5 1.0
N D:ALA646 4.8 27.7 1.0
CA D:ASP645 4.9 28.1 1.0

Magnesium binding site 5 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1301

b:20.0
occ:1.00
 O2B E:TPP1303 2.1 28.7 1.0
OD1 E:ASN678 2.2 38.1 1.0
O E:ILE680 2.3 34.0 1.0
O1A E:TPP1303 2.3 31.8 1.0
OD1 E:ASP645 2.4 54.5 1.0
CG E:ASP645 3.2 46.9 1.0
CG E:ASN678 3.2 26.1 1.0
OD2 E:ASP645 3.5 54.2 1.0
C E:ILE680 3.5 27.1 1.0
PB E:TPP1303 3.5 19.4 1.0
PA E:TPP1303 3.6 21.1 1.0
ND2 E:ASN678 3.7 28.8 1.0
O3A E:TPP1303 3.8 27.9 1.0
N E:ILE680 4.0 28.4 1.0
N E:ASP645 4.3 27.0 1.0
O3B E:TPP1303 4.3 29.2 1.0
N E:ASN678 4.3 26.8 1.0
CA E:ILE680 4.4 27.4 1.0
O E:VAL676 4.4 31.9 1.0
N E:GLY681 4.4 29.8 1.0
CB E:ASN678 4.5 26.9 1.0
CB E:ASP645 4.5 37.4 1.0
O1B E:TPP1303 4.5 27.9 1.0
O7 E:TPP1303 4.6 28.9 1.0
CA E:GLY681 4.6 29.3 1.0
N E:GLN679 4.6 27.4 1.0
C E:ASN678 4.6 27.3 1.0
O E:GLY681 4.7 52.2 1.0
CG2 E:ILE680 4.7 36.6 1.0
O2A E:TPP1303 4.7 30.9 1.0
CA E:ASN678 4.7 24.7 1.0
N E:ALA646 4.8 27.8 1.0
CA E:ASP645 4.9 28.2 1.0

Magnesium binding site 6 out of 6 in 8p5t

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


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 Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1301

b:19.9
occ:1.00
 O2B F:TPP1303 2.1 28.8 1.0
OD1 F:ASN678 2.2 37.7 1.0
O F:ILE680 2.3 34.3 1.0
O2A F:TPP1303 2.3 31.8 1.0
OD1 F:ASP645 2.4 54.6 1.0
CG F:ASP645 3.2 46.9 1.0
CG F:ASN678 3.2 25.8 1.0
OD2 F:ASP645 3.5 54.4 1.0
C F:ILE680 3.5 27.2 1.0
PB F:TPP1303 3.5 19.5 1.0
PA F:TPP1303 3.6 21.3 1.0
ND2 F:ASN678 3.7 28.5 1.0
O3A F:TPP1303 3.8 27.9 1.0
N F:ILE680 4.0 28.4 1.0
O1B F:TPP1303 4.3 29.6 1.0
N F:ASP645 4.3 27.2 1.0
N F:ASN678 4.3 26.6 1.0
CA F:ILE680 4.4 27.4 1.0
O F:VAL676 4.4 32.0 1.0
N F:GLY681 4.4 29.7 1.0
CB F:ASN678 4.5 26.7 1.0
CB F:ASP645 4.5 37.5 1.0
O3B F:TPP1303 4.5 27.9 1.0
CA F:GLY681 4.6 29.2 1.0
O7 F:TPP1303 4.6 29.0 1.0
N F:GLN679 4.6 27.2 1.0
C F:ASN678 4.6 27.0 1.0
O F:GLY681 4.7 52.1 1.0
O1A F:TPP1303 4.7 30.9 1.0
CG2 F:ILE680 4.7 36.7 1.0
CA F:ASN678 4.7 24.5 1.0
N F:ALA646 4.8 27.9 1.0
CA F:ASP645 4.9 28.3 1.0

Reference:

L.Yang, T.Wagner, A.Mechaly, A.Boyko, E.Bruch, D.Megrian, F.Gubellini, P.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 15:53:16 2024

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