Magnesium in PDB 2g28: E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex

All present enzymatic activity of E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex:
1.2.4.1;

The structure of E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex, PDB code: 2g28 was solved by W.Furey, P.Arjunan, K.Chandrasekhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.77 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.990, 143.200, 82.530, 90.00, 102.61, 90.00
R / Rfree (%)	21.6 / 24

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex (pdb code 2g28). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex, PDB code: 2g28:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg888 b:19.7 occ:1.00 OD1 B:ASP230 2.0 15.8 1.0 O1A A:TDK887 2.0 20.9 1.0 O B:GLN262 2.0 22.7 1.0 O1B A:TDK887 2.1 20.9 1.0 O A:HOH910 2.1 16.3 1.0 OD1 B:ASN260 2.2 18.8 1.0 CG B:ASP230 3.1 15.8 1.0 CG B:ASN260 3.1 18.7 1.0 C B:GLN262 3.2 22.8 1.0 PA A:TDK887 3.3 21.1 1.0 PB A:TDK887 3.4 21.0 1.0 ND2 B:ASN260 3.5 18.8 1.0 O3A A:TDK887 3.6 21.0 1.0 OD2 B:ASP230 3.7 15.8 1.0 O2B A:TDK887 3.8 20.8 1.0 N B:GLN262 3.8 21.6 1.0 N B:ASP230 3.9 15.9 1.0 CA B:GLN262 4.0 22.4 1.0 N B:GLY231 4.0 16.0 1.0 O B:ASN258 4.1 16.2 1.0 O7 A:TDK887 4.2 21.4 1.0 N B:ARG263 4.2 23.3 1.0 CB B:ASP230 4.4 15.8 1.0 O2A A:TDK887 4.4 20.9 1.0 CA B:ARG263 4.5 24.0 1.0 CA B:ASP230 4.5 15.9 1.0 N B:ASN260 4.5 18.1 1.0 CB B:ASN260 4.5 18.6 1.0 O3B A:TDK887 4.6 21.1 1.0 CB B:GLN262 4.7 22.7 1.0 N B:LEU261 4.7 19.7 1.0 C B:ASP230 4.8 15.9 1.0 NZ B:LYS392 4.8 22.2 1.0 C B:GLY229 4.8 16.0 1.0 CA B:GLY229 4.9 16.0 1.0 CG2 B:VAL268 4.9 21.7 1.0 C B:LEU261 4.9 21.0 1.0 CA B:GLY231 4.9 16.1 1.0 CA B:ASN260 4.9 18.7 1.0 C B:ASN260 5.0 19.1 1.0

Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Pyruvate Dehydrogenase H407A Variant Phosphonolactylthiamin Diphosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg888 b:18.9 occ:1.00 O1B B:TDK887 2.0 19.7 1.0 O1A B:TDK887 2.0 19.7 1.0 O A:GLN262 2.0 22.6 1.0 OD1 A:ASP230 2.1 16.8 1.0 OD1 A:ASN260 2.2 18.4 1.0 O A:HOH890 2.2 16.2 1.0 CG A:ASN260 3.1 18.4 1.0 PA B:TDK887 3.2 19.7 1.0 PB B:TDK887 3.2 19.6 1.0 C A:GLN262 3.2 22.6 1.0 CG A:ASP230 3.3 16.7 1.0 ND2 A:ASN260 3.4 18.4 1.0 O3A B:TDK887 3.5 19.7 1.0 O2B B:TDK887 3.6 19.9 1.0 OD2 A:ASP230 3.9 16.8 1.0 N A:GLN262 3.9 21.6 1.0 N A:ASP230 4.0 16.2 1.0 CA A:GLN262 4.1 22.4 1.0 N A:GLY231 4.1 16.5 1.0 O7 B:TDK887 4.1 20.5 1.0 O A:ASN258 4.1 16.7 1.0 N A:ARG263 4.2 23.0 1.0 O2A B:TDK887 4.4 19.8 1.0 CA A:ARG263 4.4 23.6 1.0 O3B B:TDK887 4.4 19.9 1.0 CB A:ASN260 4.5 18.5 1.0 CB A:ASP230 4.6 16.4 1.0 N A:ASN260 4.6 18.2 1.0 CA A:ASP230 4.7 16.4 1.0 NZ A:LYS392 4.7 22.5 1.0 CB A:GLN262 4.7 22.7 1.0 N A:LEU261 4.7 19.7 1.0 C A:GLY229 4.9 16.2 1.0 C A:ASP230 4.9 16.5 1.0 CA A:GLY229 4.9 16.1 1.0 CA A:ASN260 4.9 18.7 1.0 C A:ASN260 4.9 19.2 1.0 C A:LEU261 5.0 21.0 1.0 CA A:GLY231 5.0 16.5 1.0

P.Arjunan, M.Sax, A.Brunskill, K.Chandrasekhar, N.Nemeria, S.Zhang, F.Jordan, W.Furey. A Thiamin-Bound, Pre-Decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals Novel Structural Features in the Covalently Bound Adduct. J.Biol.Chem. V. 281 15296 2006.
ISSN: ISSN 0021-9258
PubMed: 16531404
DOI: 10.1074/JBC.M600656200