Magnesium in PDB 2ozl: Human Pyruvate Dehydrogenase S264E Variant

All present enzymatic activity of Human Pyruvate Dehydrogenase S264E Variant:
1.2.4.1;

The structure of Human Pyruvate Dehydrogenase S264E Variant, PDB code: 2ozl was solved by E.M.Ciszak, P.M.Dominiak, M.S.Patel, L.G.Korotchkina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.900, 126.400, 190.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.1

The structure of Human Pyruvate Dehydrogenase S264E Variant also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Human Pyruvate Dehydrogenase S264E Variant (pdb code 2ozl). 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 S264E Variant, PDB code: 2ozl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Pyruvate Dehydrogenase S264E Variant


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 S264E Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2331 b:5.0 occ:1.00 OD1 A:ASN196 2.3 7.2 1.0 O A:TYR198 2.3 7.2 1.0 OD2 A:ASP167 2.3 8.7 1.0 O2A A:TPP2330 2.4 5.5 1.0 O1B A:TPP2330 2.4 7.2 1.0 O A:HOH2332 2.4 6.3 1.0 CG A:ASP167 2.9 10.1 1.0 OD1 A:ASP167 3.0 8.7 1.0 CG A:ASN196 3.1 7.6 1.0 C A:TYR198 3.3 8.5 1.0 ND2 A:ASN196 3.5 5.6 1.0 PA A:TPP2330 3.5 8.9 1.0 PB A:TPP2330 3.5 10.3 1.0 O3A A:TPP2330 3.6 7.4 1.0 N A:TYR198 4.0 7.3 1.0 N A:ASP167 4.0 5.8 1.0 O A:HOH2333 4.1 10.5 1.0 O2B A:TPP2330 4.1 12.6 1.0 N A:GLY199 4.2 8.0 1.0 CA A:TYR198 4.2 9.4 1.0 N A:ASN196 4.2 5.3 1.0 CA A:GLY199 4.2 10.4 1.0 O7 A:TPP2330 4.3 7.5 1.0 CB A:ASP167 4.3 5.8 1.0 N A:GLY168 4.4 6.0 1.0 CB A:ASN196 4.5 6.4 1.0 O A:GLU194 4.5 7.6 1.0 C A:ASN196 4.7 6.2 1.0 O1A A:TPP2330 4.7 6.5 1.0 CA A:ASP167 4.7 6.5 1.0 CA A:ASN196 4.7 6.6 1.0 N A:ARG197 4.7 6.7 1.0 O3B A:TPP2330 4.7 11.9 1.0 CA A:GLY166 4.8 5.6 1.0 C A:GLY166 4.9 6.8 1.0

Magnesium binding site 2 out of 2 in the Human Pyruvate Dehydrogenase S264E Variant


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 S264E Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1331 b:5.0 occ:1.00 O C:TYR198 2.3 10.8 1.0 OD1 C:ASN196 2.3 5.7 1.0 O C:HOH1332 2.3 5.8 1.0 OD2 C:ASP167 2.3 13.1 1.0 O2A C:TPP1330 2.4 5.0 1.0 O1B C:TPP1330 2.4 11.8 1.0 CG C:ASP167 3.0 11.1 1.0 OD1 C:ASP167 3.1 12.2 1.0 CG C:ASN196 3.1 8.0 1.0 C C:TYR198 3.3 12.3 1.0 ND2 C:ASN196 3.4 6.4 1.0 PA C:TPP1330 3.5 8.2 1.0 PB C:TPP1330 3.5 10.0 1.0 O3A C:TPP1330 3.5 11.2 1.0 O2B C:TPP1330 4.0 14.0 1.0 N C:ASP167 4.0 6.2 1.0 N C:TYR198 4.0 12.3 1.0 O C:HOH1333 4.1 10.2 1.0 N C:GLY199 4.2 12.5 1.0 O7 C:TPP1330 4.2 10.3 1.0 CA C:TYR198 4.2 12.7 1.0 CA C:GLY199 4.2 13.2 1.0 N C:ASN196 4.2 8.2 1.0 CB C:ASP167 4.3 9.2 1.0 N C:GLY168 4.4 6.2 1.0 O C:GLU194 4.4 8.2 1.0 CB C:ASN196 4.5 7.2 1.0 O1A C:TPP1330 4.6 9.1 1.0 CA C:ASP167 4.7 6.7 1.0 C C:ASN196 4.7 9.5 1.0 CA C:ASN196 4.7 8.3 1.0 O3B C:TPP1330 4.7 12.8 1.0 CA C:GLY166 4.8 6.0 1.0 N C:ARG197 4.8 12.1 1.0 C C:GLY166 4.8 5.7 1.0

F.Seifert, E.M.Ciszak, L.G.Korotchkina, R.Golbik, M.Spinka, P.M.Dominiak, S.Sidhu, J.Brauer, M.S.Patel, K.Tittmann. Phosphorylation of Serine 264 Impedes Active Site Accessibility in the E1 Component of the Human Pyruvate Dehydrogenase Multienzyme Complex Biochemistry V. 46 6277 2007.
ISSN: ISSN 0006-2960
PubMed: 17474719
DOI: 10.1021/BI700083Z