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Magnesium in PDB 8p5s: Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum

Enzymatic activity of Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum

All present enzymatic activity of Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum:
1.2.4.2; 2.3.1.61;

Protein crystallography data

The structure of Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum, PDB code: 8p5s was solved by L.Yang, A.Boyko, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.53 / 2.46
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 150.987, 150.987, 314.335, 90, 90, 120
R / Rfree (%) 20.4 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum (pdb code 8p5s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum, PDB code: 8p5s:

Magnesium binding site 1 out of 1 in 8p5s

Go back to Magnesium Binding Sites List in 8p5s
Magnesium binding site 1 out of 1 in the Crystal 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 Crystal Structure of the Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1305

b:36.6
occ:1.00
 O2A A:TPP1304 2.0 54.2 1.0
O3B A:TPP1304 2.1 54.1 1.0
OD1 A:ASN678 2.2 49.4 1.0
O A:ILE680 2.2 53.5 1.0
OD1 A:ASP645 2.2 49.1 1.0
O A:HOH1405 2.5 37.6 1.0
CG A:ASP645 3.1 49.2 1.0
PA A:TPP1304 3.1 54.6 1.0
PB A:TPP1304 3.2 54.6 1.0
CG A:ASN678 3.2 48.2 1.0
O3A A:TPP1304 3.3 54.9 1.0
C A:ILE680 3.4 53.1 1.0
OD2 A:ASP645 3.5 52.1 1.0
ND2 A:ASN678 3.7 48.3 1.0
O1B A:TPP1304 3.8 54.6 1.0
N A:ASP645 3.9 42.9 1.0
O7 A:TPP1304 4.1 54.5 1.0
N A:ILE680 4.2 50.8 1.0
N A:GLY681 4.3 53.4 1.0
N A:ASN678 4.3 45.6 1.0
O A:VAL676 4.3 43.4 1.0
N A:ALA646 4.3 42.0 1.0
O1A A:TPP1304 4.3 54.9 1.0
CA A:GLY681 4.3 54.0 1.0
CB A:ASP645 4.4 45.2 1.0
CA A:ILE680 4.4 51.7 1.0
O2B A:TPP1304 4.5 54.6 1.0
CB A:ASN678 4.5 46.1 1.0
CA A:ASP645 4.6 43.2 1.0
C A:GLY644 4.7 42.5 1.0
CA A:ASN678 4.7 46.0 1.0
CA A:GLY644 4.8 41.8 1.0
CG2 A:ILE680 4.8 52.4 1.0
C A:ASN678 4.8 47.2 1.0
N A:GLN679 4.8 48.3 1.0
CB A:ALA646 4.8 42.4 1.0
C A:ASP645 5.0 42.9 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: Thu Dec 28 10:05:28 2023

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