Atomistry » Magnesium » PDB 8ox6-8pjb » 8p5t
Atomistry »
  Magnesium »
    PDB 8ox6-8pjb »
      8p5t »

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

Go back to Magnesium Binding Sites List in 8p5t
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

Go back to Magnesium Binding Sites List in 8p5t
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

Go back to Magnesium Binding Sites List in 8p5t
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

Go back to Magnesium Binding Sites List in 8p5t
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

Go back to Magnesium Binding Sites List in 8p5t
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

Go back to Magnesium Binding Sites List in 8p5t
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: Thu Dec 28 10:05:26 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy