Magnesium in PDB 8p5w: Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate

Enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate

All present enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate:
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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate (pdb code 8p5w). 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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate, PDB code: 8p5w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:22.1
occ:1.00
 OD1 A:ASN678 2.1 35.1 1.0
O3B A:QSP1303 2.1 25.8 1.0
O A:ILE680 2.4 32.2 1.0
OD1 A:ASP645 2.5 48.8 1.0
O1A A:QSP1303 2.5 28.0 1.0
CG A:ASP645 3.2 43.8 1.0
CG A:ASN678 3.2 27.1 1.0
PB A:QSP1303 3.4 19.8 1.0
OD2 A:ASP645 3.5 47.4 1.0
O3A A:QSP1303 3.6 24.5 1.0
C A:ILE680 3.6 27.9 1.0
PA A:QSP1303 3.6 22.9 1.0
ND2 A:ASN678 3.7 29.7 1.0
O1B A:QSP1303 4.0 25.8 1.0
N A:ILE680 4.1 27.8 1.0
N A:ASP645 4.2 27.8 1.0
N A:ASN678 4.3 26.4 1.0
O A:VAL676 4.3 32.7 1.0
CB A:ASP645 4.5 36.7 1.0
CA A:ILE680 4.5 27.4 1.0
N A:GLY681 4.5 30.3 1.0
CB A:ASN678 4.5 26.3 1.0
O7 A:QSP1303 4.6 27.8 1.0
O2B A:QSP1303 4.6 24.9 1.0
CA A:GLY681 4.6 31.0 1.0
O2A A:QSP1303 4.6 28.3 1.0
N A:GLN679 4.7 25.6 1.0
CA A:ASN678 4.7 24.6 1.0
N A:ALA646 4.7 28.5 1.0
O A:GLY681 4.7 46.9 1.0
C A:ASN678 4.7 25.5 1.0
CG2 A:ILE680 4.8 33.4 1.0
CA A:ASP645 4.8 29.6 1.0

Magnesium binding site 2 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:21.1
occ:1.00
 O3B B:QSP1303 2.1 25.6 1.0
OD1 B:ASN678 2.1 34.4 1.0
O B:ILE680 2.4 32.6 1.0
O1A B:QSP1303 2.4 28.4 1.0
OD1 B:ASP645 2.4 48.5 1.0
CG B:ASP645 3.2 43.6 1.0
CG B:ASN678 3.2 26.7 1.0
PB B:QSP1303 3.4 19.8 1.0
OD2 B:ASP645 3.4 47.2 1.0
C B:ILE680 3.5 28.3 1.0
PA B:QSP1303 3.6 23.2 1.0
O3A B:QSP1303 3.6 24.6 1.0
ND2 B:ASN678 3.7 29.2 1.0
N B:ILE680 4.1 27.8 1.0
O1B B:QSP1303 4.1 25.6 1.0
N B:ASP645 4.2 27.7 1.0
N B:ASN678 4.3 26.3 1.0
O B:VAL676 4.3 32.7 1.0
CB B:ASP645 4.5 36.6 1.0
CA B:ILE680 4.5 27.5 1.0
N B:GLY681 4.5 30.7 1.0
CB B:ASN678 4.5 26.1 1.0
O2B B:QSP1303 4.6 25.1 1.0
CA B:GLY681 4.6 31.5 1.0
O7 B:QSP1303 4.6 28.2 1.0
O2A B:QSP1303 4.6 28.7 1.0
N B:GLN679 4.6 25.4 1.0
CA B:ASN678 4.7 24.4 1.0
N B:ALA646 4.7 28.7 1.0
O B:GLY681 4.7 47.7 1.0
C B:ASN678 4.7 25.4 1.0
CG2 B:ILE680 4.8 33.5 1.0
CA B:ASP645 4.8 29.6 1.0

Magnesium binding site 3 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:22.5
occ:1.00
 OD1 C:ASN678 2.1 34.7 1.0
O3B C:QSP1303 2.1 26.1 1.0
O C:ILE680 2.4 32.7 1.0
OD1 C:ASP645 2.5 49.6 1.0
O1A C:QSP1303 2.5 28.6 1.0
CG C:ASP645 3.2 44.5 1.0
CG C:ASN678 3.2 27.0 1.0
PB C:QSP1303 3.4 20.1 1.0
OD2 C:ASP645 3.5 48.0 1.0
C C:ILE680 3.6 28.5 1.0
O3A C:QSP1303 3.6 24.8 1.0
PA C:QSP1303 3.6 23.3 1.0
ND2 C:ASN678 3.7 29.5 1.0
O1B C:QSP1303 4.1 25.8 1.0
N C:ILE680 4.1 27.9 1.0
N C:ASP645 4.2 28.1 1.0
N C:ASN678 4.3 26.6 1.0
O C:VAL676 4.3 32.5 1.0
CA C:ILE680 4.5 27.8 1.0
N C:GLY681 4.5 30.9 1.0
CB C:ASP645 4.5 37.3 1.0
CB C:ASN678 4.5 26.3 1.0
O7 C:QSP1303 4.6 28.3 1.0
O2B C:QSP1303 4.6 25.6 1.0
CA C:GLY681 4.6 31.7 1.0
O2A C:QSP1303 4.6 28.7 1.0
N C:GLN679 4.7 25.5 1.0
CA C:ASN678 4.7 24.6 1.0
N C:ALA646 4.7 28.9 1.0
O C:GLY681 4.7 47.4 1.0
C C:ASN678 4.7 25.4 1.0
CG2 C:ILE680 4.8 33.6 1.0
CA C:ASP645 4.8 30.1 1.0

Magnesium binding site 4 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1301

b:21.7
occ:1.00
 O3B D:QSP1303 2.1 25.8 1.0
OD1 D:ASN678 2.1 34.8 1.0
O D:ILE680 2.4 32.7 1.0
OD1 D:ASP645 2.4 48.9 1.0
O1A D:QSP1303 2.5 28.7 1.0
CG D:ASP645 3.2 43.9 1.0
CG D:ASN678 3.2 27.1 1.0
PB D:QSP1303 3.4 19.8 1.0
OD2 D:ASP645 3.4 47.5 1.0
C D:ILE680 3.6 28.4 1.0
PA D:QSP1303 3.6 23.2 1.0
O3A D:QSP1303 3.6 24.6 1.0
ND2 D:ASN678 3.7 29.6 1.0
O1B D:QSP1303 4.1 25.5 1.0
N D:ILE680 4.1 27.7 1.0
N D:ASP645 4.2 27.9 1.0
N D:ASN678 4.2 26.5 1.0
O D:VAL676 4.3 32.8 1.0
CB D:ASP645 4.4 37.0 1.0
CA D:ILE680 4.5 27.5 1.0
N D:GLY681 4.5 30.7 1.0
CB D:ASN678 4.5 26.3 1.0
O2B D:QSP1303 4.6 25.2 1.0
CA D:GLY681 4.6 31.5 1.0
O7 D:QSP1303 4.6 28.2 1.0
N D:GLN679 4.6 25.4 1.0
O2A D:QSP1303 4.6 28.8 1.0
CA D:ASN678 4.7 24.5 1.0
N D:ALA646 4.7 28.9 1.0
O D:GLY681 4.7 47.4 1.0
C D:ASN678 4.7 25.4 1.0
CG2 D:ILE680 4.8 33.1 1.0
CA D:ASP645 4.8 29.9 1.0

Magnesium binding site 5 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1301

b:21.8
occ:1.00
 O3B E:QSP1303 2.1 25.4 1.0
OD1 E:ASN678 2.1 34.6 1.0
O E:ILE680 2.4 32.2 1.0
OD1 E:ASP645 2.4 48.7 1.0
O1A E:QSP1303 2.5 28.1 1.0
CG E:ASP645 3.2 43.6 1.0
CG E:ASN678 3.2 26.7 1.0
PB E:QSP1303 3.4 19.7 1.0
OD2 E:ASP645 3.4 47.2 1.0
C E:ILE680 3.5 28.1 1.0
O3A E:QSP1303 3.6 24.4 1.0
PA E:QSP1303 3.6 23.0 1.0
ND2 E:ASN678 3.7 29.2 1.0
N E:ILE680 4.1 27.6 1.0
O1B E:QSP1303 4.1 25.4 1.0
N E:ASP645 4.2 27.6 1.0
N E:ASN678 4.3 26.1 1.0
O E:VAL676 4.4 32.4 1.0
CA E:ILE680 4.4 27.3 1.0
N E:GLY681 4.4 30.5 1.0
CB E:ASP645 4.5 36.5 1.0
CB E:ASN678 4.5 26.0 1.0
O2B E:QSP1303 4.6 24.9 1.0
CA E:GLY681 4.6 31.3 1.0
O7 E:QSP1303 4.6 28.1 1.0
N E:GLN679 4.6 25.2 1.0
O2A E:QSP1303 4.7 28.4 1.0
N E:ALA646 4.7 28.5 1.0
CA E:ASN678 4.7 24.2 1.0
O E:GLY681 4.7 47.4 1.0
C E:ASN678 4.7 25.1 1.0
CG2 E:ILE680 4.8 33.4 1.0
CA E:ASP645 4.8 29.4 1.0

Magnesium binding site 6 out of 6 in 8p5w

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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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate


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 Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1301

b:21.4
occ:1.00
 OD1 F:ASN678 2.1 34.8 1.0
O3B F:QSP1303 2.1 25.6 1.0
O F:ILE680 2.4 32.5 1.0
O1A F:QSP1303 2.4 28.2 1.0
OD1 F:ASP645 2.5 49.1 1.0
CG F:ASP645 3.2 44.2 1.0
CG F:ASN678 3.2 27.0 1.0
PB F:QSP1303 3.4 19.6 1.0
OD2 F:ASP645 3.5 47.8 1.0
C F:ILE680 3.6 28.3 1.0
PA F:QSP1303 3.6 23.0 1.0
O3A F:QSP1303 3.6 24.5 1.0
ND2 F:ASN678 3.7 29.6 1.0
O1B F:QSP1303 4.0 25.4 1.0
N F:ILE680 4.1 27.9 1.0
N F:ASP645 4.2 28.0 1.0
N F:ASN678 4.2 26.5 1.0
O F:VAL676 4.3 32.7 1.0
CB F:ASP645 4.5 37.1 1.0
CA F:ILE680 4.5 27.6 1.0
N F:GLY681 4.5 30.8 1.0
CB F:ASN678 4.5 26.3 1.0
O7 F:QSP1303 4.6 28.0 1.0
CA F:GLY681 4.6 31.5 1.0
O2B F:QSP1303 4.6 24.8 1.0
O2A F:QSP1303 4.6 28.6 1.0
N F:GLN679 4.7 25.6 1.0
CA F:ASN678 4.7 24.6 1.0
N F:ALA646 4.7 28.8 1.0
O F:GLY681 4.7 47.8 1.0
C F:ASN678 4.7 25.6 1.0
CG2 F:ILE680 4.8 33.3 1.0
CA F:ASP645 4.8 29.9 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 15:55:51 2024

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