Magnesium in PDB 1ni4: Human Pyruvate Dehydrogenase

All present enzymatic activity of Human Pyruvate Dehydrogenase:
1.2.4.1;

The structure of Human Pyruvate Dehydrogenase, PDB code: 1ni4 was solved by E.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.17 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.337, 126.889, 190.638, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.4

The structure of Human Pyruvate Dehydrogenase also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Human Pyruvate Dehydrogenase (pdb code 1ni4). 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, PDB code: 1ni4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Pyruvate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1331 b:5.9 occ:1.00 O C:HOH2332 2.3 11.3 1.0 OD1 C:ASN196 2.3 11.8 1.0 O1B C:TPP1330 2.4 15.6 1.0 O C:TYR198 2.4 22.8 1.0 O2A C:TPP1330 2.4 8.5 1.0 OD2 C:ASP167 2.5 16.2 1.0 OD1 C:ASP167 3.1 17.1 1.0 CG C:ASP167 3.1 14.3 1.0 CG C:ASN196 3.1 11.9 1.0 ND2 C:ASN196 3.3 10.9 1.0 C C:TYR198 3.3 22.9 1.0 PB C:TPP1330 3.5 15.3 1.0 PA C:TPP1330 3.5 10.2 1.0 O3A C:TPP1330 3.6 12.8 1.0 N C:TYR198 4.0 20.1 1.0 N C:ASP167 4.0 6.0 1.0 O2B C:TPP1330 4.1 16.3 1.0 O C:HOH2333 4.1 13.9 1.0 N C:GLY199 4.1 24.8 1.0 CA C:TYR198 4.2 21.5 1.0 CA C:GLY199 4.3 26.8 1.0 N C:ASN196 4.3 12.1 1.0 O7 C:TPP1330 4.3 16.0 1.0 CB C:ASN196 4.4 11.1 1.0 CB C:ASP167 4.4 11.3 1.0 O C:GLU194 4.4 14.2 1.0 N C:GLY168 4.4 9.5 1.0 C C:ASN196 4.7 13.1 1.0 O1A C:TPP1330 4.7 9.9 1.0 CA C:ASN196 4.7 12.8 1.0 CA C:GLY166 4.7 5.9 1.0 CA C:ASP167 4.7 8.7 1.0 O3B C:TPP1330 4.7 18.0 1.0 O C:HOH2334 4.8 28.9 1.0 C C:GLY166 4.8 5.8 1.0 N C:ARG197 4.9 15.9 1.0 O C:ASN196 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Human Pyruvate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2331 b:5.3 occ:1.00 OD1 A:ASN196 2.2 9.6 1.0 O A:TYR198 2.3 13.6 1.0 O2A A:TPP2330 2.4 6.9 1.0 O1B A:TPP2330 2.4 6.2 1.0 O A:HOH2331 2.4 10.6 1.0 OD2 A:ASP167 2.4 13.8 1.0 OD1 A:ASP167 2.9 11.2 1.0 CG A:ASP167 2.9 11.7 1.0 CG A:ASN196 3.1 6.9 1.0 C A:TYR198 3.3 12.9 1.0 ND2 A:ASN196 3.5 5.3 1.0 PA A:TPP2330 3.5 6.8 1.0 PB A:TPP2330 3.6 11.3 1.0 O3A A:TPP2330 3.6 9.7 1.0 N A:TYR198 3.9 10.7 1.0 N A:ASP167 4.0 6.9 1.0 N A:GLY199 4.1 15.0 1.0 N A:ASN196 4.2 6.5 1.0 CA A:TYR198 4.2 12.0 1.0 CA A:GLY199 4.2 17.9 1.0 O A:HOH2332 4.2 15.7 1.0 O2B A:TPP2330 4.3 12.6 1.0 CB A:ASP167 4.3 8.4 1.0 O7 A:TPP2330 4.3 8.6 1.0 N A:GLY168 4.3 7.0 1.0 CB A:ASN196 4.4 5.9 1.0 O A:GLU194 4.5 9.2 1.0 CA A:ASN196 4.6 7.2 1.0 CA A:ASP167 4.6 8.0 1.0 C A:ASN196 4.7 8.2 1.0 O1A A:TPP2330 4.7 9.4 1.0 N A:ARG197 4.7 7.8 1.0 O3B A:TPP2330 4.7 13.1 1.0 CA A:GLY166 4.8 6.9 1.0 C A:GLY166 4.8 8.2 1.0

E.M.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel. Structural Basis For Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed By Human Pyruvate Dehydrogenase J.Biol.Chem. V. 278 21240 2003.
ISSN: ISSN 0021-9258
PubMed: 12651851
DOI: 10.1074/JBC.M300339200