Magnesium in PDB 8i0k: Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex

All present enzymatic activity of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex:
1.2.4.2;

The structure of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex (pdb code 8i0k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex, PDB code: 8i0k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:33.3 occ:1.00 OD1 A:ASN444 2.0 33.2 1.0 O3B A:TPP1102 2.0 38.2 1.0 OD1 A:ASP411 2.1 32.3 1.0 O2A A:TPP1102 2.1 38.2 1.0 O A:ILE446 2.5 36.0 1.0 CG A:ASN444 2.9 33.2 1.0 PB A:TPP1102 3.1 38.2 1.0 CG A:ASP411 3.2 32.3 1.0 PA A:TPP1102 3.3 38.2 1.0 ND2 A:ASN444 3.3 33.2 1.0 O3A A:TPP1102 3.4 38.2 1.0 C A:ILE446 3.7 36.0 1.0 OD2 A:ASP411 3.7 32.3 1.0 O2B A:TPP1102 3.8 38.2 1.0 N A:ASP411 4.1 32.3 1.0 N A:ILE446 4.2 36.0 1.0 O A:VAL442 4.2 30.0 1.0 N A:ASN444 4.3 33.2 1.0 CB A:ASN444 4.3 33.2 1.0 O1A A:TPP1102 4.3 38.2 1.0 O7 A:TPP1102 4.3 38.2 1.0 O1B A:TPP1102 4.4 38.2 1.0 CB A:ASP411 4.5 32.3 1.0 N A:ALA412 4.5 31.8 1.0 CA A:ILE446 4.6 36.0 1.0 N A:GLY447 4.6 38.3 1.0 CA A:ASN444 4.6 33.2 1.0 CA A:GLY447 4.6 38.3 1.0 N A:GLN445 4.7 36.4 1.0 C A:ASN444 4.7 33.2 1.0 CG2 A:ILE446 4.7 36.0 1.0 CA A:ASP411 4.8 32.3 1.0 O A:GLY447 4.9 38.3 1.0 C A:GLY410 5.0 28.6 1.0

Magnesium binding site 2 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase(E1) with Tcaim Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1101 b:32.0 occ:1.00 OD1 B:ASN444 2.0 33.8 1.0 OD1 B:ASP411 2.1 32.8 1.0 O1A B:8EL1102 2.2 39.5 1.0 O B:ILE446 2.5 36.5 1.0 O2B B:8EL1102 2.8 39.5 1.0 CG B:ASN444 2.9 33.8 1.0 CG B:ASP411 3.2 32.8 1.0 ND2 B:ASN444 3.3 33.8 1.0 O1B B:8EL1102 3.3 39.5 1.0 PA B:8EL1102 3.4 39.5 1.0 PB B:8EL1102 3.4 39.5 1.0 O3A B:8EL1102 3.6 39.5 1.0 C B:ILE446 3.7 36.5 1.0 OD2 B:ASP411 3.7 32.8 1.0 N B:ASP411 4.1 32.8 1.0 N B:ILE446 4.2 36.5 1.0 O B:VAL442 4.2 30.1 1.0 N B:ASN444 4.3 33.8 1.0 CB B:ASN444 4.3 33.8 1.0 O7 B:8EL1102 4.4 39.5 1.0 CB B:ASP411 4.5 32.8 1.0 O2A B:8EL1102 4.5 39.5 1.0 N B:ALA412 4.5 32.1 1.0 CA B:ILE446 4.6 36.5 1.0 N B:GLY447 4.6 38.9 1.0 CA B:ASN444 4.6 33.8 1.0 CA B:GLY447 4.6 38.9 1.0 N B:GLN445 4.7 36.8 1.0 C B:ASN444 4.7 33.8 1.0 CG2 B:ILE446 4.7 36.5 1.0 CA B:ASP411 4.8 32.8 1.0 O B:GLY447 4.9 38.9 1.0 O3B B:8EL1102 4.9 39.5 1.0 C B:GLY410 5.0 30.9 1.0

X.Yu, W.Yang, Y.H.Zhong, X.M.Ma, Y.Z.Gao. Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) with Tcaim Complex To Be Published.