Magnesium in PDB 6cfo: Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate

All present enzymatic activity of Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate:
1.2.4.1;

The structure of Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate, PDB code: 6cfo was solved by P.Arjunan, M.J.Whitley, W.Furey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.58 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.270, 120.730, 129.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.5

The binding sites of Magnesium atom in the Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate (pdb code 6cfo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate, PDB code: 6cfo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:28.2 occ:1.00 O12 A:A5X401 1.8 68.6 1.0 O23 A:A5X401 2.0 44.7 1.0 O A:TYR198 2.0 37.5 1.0 OD1 A:ASN196 2.2 47.2 1.0 OD1 A:ASP167 2.3 40.9 1.0 O A:HOH527 2.4 32.9 1.0 P1 A:A5X401 3.0 41.8 1.0 CG A:ASP167 3.1 40.9 1.0 P2 A:A5X401 3.1 44.8 1.0 CG A:ASN196 3.2 47.0 1.0 C A:TYR198 3.2 40.2 1.0 OD2 A:ASP167 3.4 41.2 1.0 O11 A:A5X401 3.4 40.9 1.0 ND2 A:ASN196 3.5 48.1 1.0 O21 A:A5X401 3.8 45.8 1.0 O5G A:A5X401 3.8 44.3 1.0 CA A:GLY199 3.9 44.2 1.0 N A:ASP167 3.9 33.6 1.0 N A:GLY199 3.9 43.1 1.0 N A:GLY168 4.1 33.5 1.0 O13 A:A5X401 4.1 40.7 1.0 O A:HOH536 4.2 51.9 1.0 N A:TYR198 4.2 42.1 1.0 CA A:TYR198 4.3 40.1 1.0 CB A:ASP167 4.3 37.9 1.0 O22 A:A5X401 4.4 43.6 1.0 N A:ASN196 4.5 42.8 1.0 CB A:ASN196 4.6 44.3 1.0 CA A:ASP167 4.6 35.3 1.0 CA A:GLY166 4.7 34.3 1.0 O A:GLU194 4.7 41.4 1.0 C A:GLY166 4.7 33.3 1.0 C A:ASP167 4.9 35.2 1.0 CA A:ASN196 4.9 43.6 1.0 N A:MET200 4.9 46.5 1.0 C A:ASN196 5.0 44.8 1.0

Magnesium binding site 2 out of 2 in the Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Pyruvate Dehydrogenase E1 Component Complex with Covalent Tdp Adduct Acetyl Phosphinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:34.9 occ:1.00 O12 C:A5X401 1.7 76.4 1.0 O23 C:A5X401 2.1 50.8 1.0 OD1 C:ASP167 2.3 49.1 1.0 O C:TYR198 2.4 58.2 1.0 O C:HOH505 2.5 0.6 1.0 OD1 C:ASN196 2.6 56.1 1.0 P1 C:A5X401 2.9 76.3 1.0 P2 C:A5X401 3.1 51.7 1.0 O11 C:A5X401 3.2 77.6 1.0 CG C:ASP167 3.3 49.4 1.0 CG C:ASN196 3.4 55.7 1.0 C C:TYR198 3.6 58.9 1.0 N C:ASP167 3.6 39.8 1.0 ND2 C:ASN196 3.7 55.3 1.0 O C:HOH511 3.7 39.6 1.0 O21 C:A5X401 3.8 52.0 1.0 OD2 C:ASP167 3.8 52.8 1.0 O5G C:A5X401 3.9 73.7 1.0 O13 C:A5X401 4.0 75.2 1.0 N C:GLY168 4.1 40.0 1.0 CA C:GLY166 4.2 38.1 1.0 CA C:GLY199 4.3 60.8 1.0 N C:GLY199 4.3 60.3 1.0 C C:GLY166 4.3 38.4 1.0 CB C:ASP167 4.4 45.2 1.0 O22 C:A5X401 4.4 52.6 1.0 O C:GLU194 4.4 42.2 1.0 CA C:ASP167 4.4 41.3 1.0 N C:TYR198 4.5 59.6 1.0 CA C:TYR198 4.6 58.4 1.0 N C:ASN196 4.7 50.7 1.0 C C:ASP167 4.8 40.2 1.0 CB C:ASN196 4.8 55.1 1.0

M.J.Whitley, P.Arjunan, N.S.Nemeria, L.G.Korotchkina, Y.H.Park, M.S.Patel, F.Jordan, W.Furey. Pyruvate Dehydrogenase Complex Deficiency Is Linked to Regulatory Loop Disorder in the Alpha V138M Variant of Human Pyruvate Dehydrogenase. J. Biol. Chem. V. 293 13204 2018.
ISSN: ESSN 1083-351X
PubMed: 29970614
DOI: 10.1074/JBC.RA118.003996