Potassium in PDB 3duf: Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex

All present enzymatic activity of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex:
1.2.4.1; 2.3.1.12;

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3duf was solved by X.Y.Pei, C.M.Titman, R.A.W.Frank, F.J.Leeper, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.44 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.247, 231.995, 92.614, 90.00, 90.74, 90.00
R / Rfree (%)	18.8 / 26.3

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Potassium atom in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex (pdb code 3duf). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3duf:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1325 b:52.7 occ:1.00 O B:ALA160 2.9 35.9 1.0 O B:ASP165 2.9 35.2 1.0 O B:ASP163 2.9 26.6 1.0 O B:ILE112 3.1 25.4 1.0 O B:HOH1335 3.1 31.4 1.0 OG1 B:THR113 3.3 29.7 1.0 C B:ILE112 3.5 23.2 1.0 N B:ILE112 3.6 30.3 1.0 C B:ASP163 3.8 33.8 1.0 C B:PRO111 3.8 30.5 1.0 CB B:ASP163 3.8 28.3 1.0 CG2 B:VAL167 4.0 33.0 1.0 C B:ALA160 4.0 34.0 1.0 C B:ASP165 4.0 32.1 1.0 CA B:ILE112 4.1 27.1 1.0 N B:THR113 4.1 22.1 1.0 O B:ILE161 4.2 33.9 1.0 CA B:ASP163 4.2 33.9 1.0 CA B:PRO111 4.2 27.1 1.0 O B:PRO111 4.2 28.0 1.0 N B:ASP163 4.3 33.5 1.0 N B:VAL167 4.3 27.8 1.0 CB B:VAL167 4.4 30.3 1.0 C B:ILE161 4.4 28.3 1.0 N B:ASP165 4.5 27.4 1.0 CB B:THR113 4.5 29.4 1.0 CA B:THR113 4.5 22.9 1.0 CA B:ILE161 4.5 29.6 1.0 CA B:PRO166 4.6 25.5 1.0 OD1 B:ASP163 4.6 31.9 1.0 C B:PRO166 4.7 26.5 1.0 CG B:ASP163 4.7 29.1 1.0 N B:ILE161 4.7 31.3 1.0 N B:PRO166 4.7 29.7 1.0 O B:MET110 4.8 33.1 1.0 N B:ASN164 4.8 28.8 1.0 CA B:ASP165 4.9 34.1 1.0 CA B:ALA160 4.9 36.7 1.0

Potassium binding site 2 out of 2 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:K1325 b:32.7 occ:1.00 O D:ASP165 2.9 35.5 1.0 O D:ALA160 2.9 29.4 1.0 O D:ILE112 3.0 23.2 1.0 O D:HOH1374 3.1 45.4 1.0 O D:ASP163 3.1 35.2 1.0 OG1 D:THR113 3.2 26.5 1.0 C D:ILE112 3.5 26.7 1.0 N D:ILE112 3.7 18.8 1.0 CG2 D:VAL167 3.8 22.3 1.0 C D:ASP165 3.9 30.4 1.0 C D:ASP163 3.9 28.2 1.0 C D:PRO111 3.9 24.4 1.0 CB D:ASP163 4.0 35.3 1.0 C D:ALA160 4.1 24.3 1.0 CA D:ILE112 4.1 22.4 1.0 N D:THR113 4.1 24.8 1.0 N D:VAL167 4.2 23.2 1.0 CB D:VAL167 4.2 14.5 1.0 O D:ILE161 4.3 37.6 1.0 CA D:PRO111 4.4 29.3 1.0 N D:ASP165 4.4 32.3 1.0 CB D:THR113 4.4 27.0 1.0 CA D:ASP163 4.4 28.5 1.0 O D:PRO111 4.4 24.7 1.0 CA D:THR113 4.5 17.9 1.0 CA D:PRO166 4.5 30.0 1.0 OD1 D:ASP163 4.6 54.1 1.0 N D:ASP163 4.6 30.9 1.0 C D:PRO166 4.6 31.8 1.0 N D:PRO166 4.6 25.8 1.0 C D:ILE161 4.6 32.0 1.0 CA D:ILE161 4.7 22.6 1.0 CG D:ASP163 4.7 42.0 1.0 N D:ASN164 4.8 28.1 1.0 CA D:ASP165 4.8 30.8 1.0 CA D:VAL167 4.8 24.2 1.0 N D:ILE161 4.9 23.0 1.0 O D:MET110 4.9 36.1 1.0 C D:ASN164 4.9 30.5 1.0

X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, B.F.Luisi. Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multienzyme Complex Structure V. 16 1860 2008.
ISSN: ISSN 0969-2126
PubMed: 19081062
DOI: 10.1016/J.STR.2008.10.009