Magnesium in PDB 2qta: E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate

All present enzymatic activity of E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate:
1.2.4.1;

The structure of E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate, PDB code: 2qta 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)	38.06 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.810, 141.830, 82.560, 90.00, 102.01, 90.00
R / Rfree (%)	21.4 / 23.7

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate (pdb code 2qta). 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 E1 Component E401K Mutant with Thiamin Diphosphate, PDB code: 2qta:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate


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 E1 Component E401K Mutant with Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg888 b:19.5 occ:1.00 OD1 A:ASN260 2.1 20.4 1.0 OD1 A:ASP230 2.1 15.5 1.0 O A:GLN262 2.2 24.8 1.0 O23 A:TDP887 2.3 21.5 1.0 O12 A:TDP887 2.3 20.8 1.0 O A:HOH936 2.3 17.7 1.0 CG A:ASN260 3.0 20.4 1.0 CG A:ASP230 3.2 15.7 1.0 P2 A:TDP887 3.3 21.5 1.0 C A:GLN262 3.4 24.8 1.0 ND2 A:ASN260 3.4 20.4 1.0 P1 A:TDP887 3.4 20.9 1.0 O11 A:TDP887 3.5 21.1 1.0 OD2 A:ASP230 3.8 15.6 1.0 N A:ASP230 3.8 15.4 1.0 O21 A:TDP887 3.9 21.5 1.0 N A:GLN262 4.0 23.8 1.0 O A:ASN258 4.0 17.4 1.0 N A:GLY231 4.1 15.1 1.0 CA A:GLN262 4.2 24.5 1.0 O5G A:TDP887 4.3 21.1 1.0 N A:ARG263 4.3 25.2 1.0 N A:ASN260 4.4 19.6 1.0 CB A:ASN260 4.4 20.3 1.0 CB A:ASP230 4.4 15.5 1.0 CA A:ASP230 4.5 15.3 1.0 NZ A:LYS392 4.5 26.9 1.0 CA A:ARG263 4.5 25.5 1.0 O13 A:TDP887 4.6 20.6 1.0 O22 A:TDP887 4.6 21.5 1.0 N A:LEU261 4.7 21.7 1.0 C A:GLY229 4.7 15.3 1.0 C A:ASP230 4.8 15.3 1.0 CA A:GLY229 4.8 15.3 1.0 CB A:GLN262 4.8 24.8 1.0 CA A:ASN260 4.8 20.4 1.0 C A:ASN260 4.8 21.0 1.0 CG2 A:VAL268 4.9 25.0 1.0 C A:LEU261 5.0 23.0 1.0 CA A:GLY231 5.0 14.8 1.0

Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase E1 Component E401K Mutant with Thiamin Diphosphate


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 E1 Component E401K Mutant with Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg888 b:18.5 occ:1.00 OD1 B:ASP230 2.1 14.2 1.0 O B:GLN262 2.1 21.3 1.0 O B:HOH902 2.1 12.6 1.0 OD1 B:ASN260 2.2 17.2 1.0 O12 B:TDP887 2.2 17.6 1.0 O23 B:TDP887 2.3 18.0 1.0 CG B:ASN260 3.1 17.5 1.0 CG B:ASP230 3.2 14.2 1.0 C B:GLN262 3.3 21.4 1.0 P2 B:TDP887 3.3 17.9 1.0 P1 B:TDP887 3.4 17.6 1.0 ND2 B:ASN260 3.4 17.5 1.0 O11 B:TDP887 3.5 17.8 1.0 O21 B:TDP887 3.7 18.1 1.0 OD2 B:ASP230 3.7 14.2 1.0 N B:ASP230 3.8 14.1 1.0 N B:GLN262 3.8 20.5 1.0 CA B:GLN262 4.0 21.2 1.0 N B:GLY231 4.0 14.1 1.0 O B:ASN258 4.0 15.8 1.0 N B:ARG263 4.3 21.8 1.0 O5G B:TDP887 4.3 17.8 1.0 CB B:ASP230 4.4 14.1 1.0 CA B:ARG263 4.4 22.2 1.0 N B:ASN260 4.5 17.3 1.0 CA B:ASP230 4.5 14.1 1.0 CB B:ASN260 4.5 17.5 1.0 O13 B:TDP887 4.5 17.5 1.0 CB B:GLN262 4.6 21.6 1.0 NZ B:LYS392 4.6 27.8 1.0 O22 B:TDP887 4.7 18.2 1.0 N B:LEU261 4.7 18.7 1.0 C B:GLY229 4.7 14.1 1.0 C B:ASP230 4.8 14.1 1.0 CA B:GLY229 4.8 14.0 1.0 CA B:ASN260 4.8 17.8 1.0 C B:ASN260 4.9 18.2 1.0 CD B:LYS392 4.9 27.7 1.0 C B:LEU261 4.9 19.9 1.0 CG2 B:VAL268 5.0 20.8 1.0 CA B:GLY231 5.0 14.0 1.0

S.Kale, P.Arjunan, W.Furey, F.Jordan. A Dynamic Loop at the Active Center of the Escherichia Coli Pyruvate Dehydrogenase Complex E1 Component Modulates Substrate Utilization and Chemical Communication with the E2 Component J.Biol.Chem. V. 282 28106 2007.
ISSN: ISSN 0021-9258
PubMed: 17635929
DOI: 10.1074/JBC.M704326200