Magnesium in PDB 7wgr: Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex

Enzymatic activity of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex

All present enzymatic activity of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex:
1.2.4.2;

Other elements in 7wgr:

The structure of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex (pdb code 7wgr). 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) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex, PDB code: 7wgr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7wgr

Go back to Magnesium Binding Sites List in 7wgr
Magnesium binding site 1 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase 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) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:24.6
occ:1.00
 OD1 A:ASN444 2.0 27.4 1.0
O2B A:TPP1103 2.0 28.2 1.0
O2A A:TPP1103 2.1 28.2 1.0
CG A:ASN444 2.5 27.4 1.0
ND2 A:ASN444 2.6 27.4 1.0
O A:ILE446 2.7 28.0 1.0
PB A:TPP1103 2.9 28.2 1.0
O3A A:TPP1103 2.9 28.2 1.0
PA A:TPP1103 2.9 28.2 1.0
OD1 A:ASP411 3.3 26.4 1.0
O3B A:TPP1103 3.4 28.2 1.0
C A:ILE446 3.9 28.0 1.0
O1A A:TPP1103 4.0 28.2 1.0
CB A:ASN444 4.0 27.4 1.0
O7 A:TPP1103 4.1 28.2 1.0
CG A:ASP411 4.2 26.4 1.0
O1B A:TPP1103 4.2 28.2 1.0
OD2 A:ASP411 4.5 26.4 1.0
N A:ILE446 4.6 28.0 1.0
CA A:GLY447 4.6 28.2 1.0
N A:ASN444 4.7 27.4 1.0
N A:GLY447 4.7 28.2 1.0
CA A:ASN444 4.8 27.4 1.0
CA A:ILE446 4.8 28.0 1.0
N A:ASP411 4.8 26.4 1.0
CG2 A:ILE446 5.0 28.0 1.0

Magnesium binding site 2 out of 2 in 7wgr

Go back to Magnesium Binding Sites List in 7wgr
Magnesium binding site 2 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase 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) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:25.1
occ:1.00
 OD1 B:ASN444 1.9 27.8 1.0
O2A B:TPP1103 2.0 27.7 1.0
O3B B:TPP1103 2.0 27.7 1.0
O B:ILE446 2.6 28.6 1.0
PB B:TPP1103 2.6 27.7 1.0
CG B:ASN444 2.7 27.8 1.0
O2B B:TPP1103 2.9 27.7 1.0
O3A B:TPP1103 2.9 27.7 1.0
ND2 B:ASN444 2.9 27.8 1.0
PA B:TPP1103 2.9 27.7 1.0
OD1 B:ASP411 3.0 26.0 1.0
C B:ILE446 3.8 28.6 1.0
O1A B:TPP1103 3.9 27.7 1.0
CB B:ASN444 4.1 27.8 1.0
O1B B:TPP1103 4.1 27.7 1.0
O7 B:TPP1103 4.1 27.7 1.0
CG B:ASP411 4.2 26.0 1.0
CA B:GLY447 4.5 28.8 1.0
N B:ILE446 4.6 28.6 1.0
N B:ASN444 4.6 27.8 1.0
N B:GLY447 4.6 28.8 1.0
N B:ASP411 4.7 26.0 1.0
CA B:ASN444 4.8 27.8 1.0
CA B:ILE446 4.8 28.6 1.0
OD2 B:ASP411 4.8 26.0 1.0
O B:VAL442 4.9 25.3 1.0
N B:ALA412 4.9 25.3 1.0
CG2 B:ILE446 5.0 28.6 1.0

Reference:

Y.Zhong, Y.Gao, D.Zhou, X.Ma, H.Chen, Y.Xu, W.Yang, X.Yu. Structural Basis For the Activity and Regulation of Human Alpha-Ketoglutarate Dehydrogenase Revealed By Cryo-Em Biochem.Biophys.Res.Commun. V. 602 120 2022.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2022.02.093
Page generated: Fri Apr 7 01:40:46 2023

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