Potassium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the Human Pyruvate Dehydrogenase (pdb code 1ni4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Human Pyruvate Dehydrogenase, PDB code: 1ni4:
Jump to Potassium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Pyruvate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:K1332 b:12.3 occ:1.00 O B:ALA160 2.8 5.3 1.0 O B:ASN165 2.9 5.3 1.0 O B:HOH1333 3.0 12.8 1.0 O B:ASP163 3.0 8.2 1.0 O B:ILE112 3.1 5.3 1.0 N B:ILE112 3.4 6.2 1.0 C B:ILE112 3.6 5.3 1.0 CG2 B:VAL113 3.7 5.3 1.0 C B:ASP163 3.8 7.6 1.0 CG2 B:VAL167 3.8 6.4 1.0 C B:PRO111 3.9 5.9 1.0 C B:ASN165 3.9 6.5 1.0 C B:ALA160 4.0 6.5 1.0 CA B:ILE112 4.0 6.2 1.0 CB B:ASP163 4.1 10.9 1.0 CA B:PRO111 4.1 6.1 1.0 N B:ASN165 4.2 7.6 1.0 O B:ILE161 4.2 6.8 1.0 CA B:ASP163 4.3 9.3 1.0 N B:VAL113 4.4 5.7 1.0 N B:VAL167 4.4 5.3 1.0 CB B:VAL167 4.4 5.3 1.0 N B:ASP163 4.4 7.4 1.0 C B:ILE161 4.5 8.0 1.0 CA B:ILE161 4.6 6.8 1.0 O B:PRO111 4.6 5.3 1.0 N B:ASN164 4.7 8.3 1.0 CB B:PRO111 4.7 5.4 1.0 CA B:ASN165 4.7 6.8 1.0 CA B:PRO166 4.7 6.0 1.0 N B:ILE161 4.7 6.7 1.0 OD1 B:ASP163 4.8 18.0 1.0 N B:PRO166 4.8 6.8 1.0 CA B:VAL113 4.8 5.7 1.0 C B:PRO166 4.8 6.6 1.0 C B:ASN164 4.8 8.6 1.0 CB B:VAL113 4.9 5.8 1.0 CG B:ASP163 4.9 16.7 1.0 CA B:ASN164 4.9 9.9 1.0 CA B:ALA160 4.9 5.7 1.0

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Pyruvate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ D:K2332 b:12.4 occ:1.00 O D:ASN165 2.8 8.3 1.0 O D:ALA160 2.9 5.3 1.0 O D:ASP163 2.9 7.8 1.0 O D:ILE112 3.1 5.3 1.0 O D:HOH2334 3.1 15.5 1.0 N D:ILE112 3.4 6.3 1.0 C D:ILE112 3.6 5.3 1.0 CG2 D:VAL113 3.7 5.3 1.0 C D:ASP163 3.8 9.7 1.0 C D:PRO111 3.8 6.7 1.0 CG2 D:VAL167 3.9 6.2 1.0 C D:ASN165 3.9 8.7 1.0 C D:ALA160 4.0 6.7 1.0 CA D:ILE112 4.0 5.5 1.0 CA D:PRO111 4.1 6.2 1.0 CB D:ASP163 4.2 13.2 1.0 N D:ASN165 4.2 8.7 1.0 O D:ILE161 4.2 10.0 1.0 N D:VAL113 4.4 5.3 1.0 CB D:VAL167 4.4 6.0 1.0 N D:VAL167 4.4 7.1 1.0 CA D:ASP163 4.4 10.3 1.0 N D:ASP163 4.5 10.0 1.0 C D:ILE161 4.5 9.0 1.0 O D:PRO111 4.6 6.4 1.0 CA D:ILE161 4.6 8.1 1.0 N D:ASN164 4.7 9.4 1.0 OD1 D:ASP163 4.7 20.8 1.0 CB D:PRO111 4.7 6.0 1.0 CA D:ASN165 4.7 9.5 1.0 CA D:PRO166 4.8 7.1 1.0 N D:ILE161 4.8 6.5 1.0 C D:ASN164 4.8 10.6 1.0 N D:PRO166 4.8 7.3 1.0 CA D:VAL113 4.8 5.3 1.0 C D:PRO166 4.8 7.8 1.0 CA D:ASN164 4.9 11.0 1.0 CB D:VAL113 4.9 5.3 1.0 CG D:ASP163 5.0 18.1 1.0 CA D:ALA160 5.0 7.3 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