Magnesium in PDB 3lq4: E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration

All present enzymatic activity of E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration:
1.2.4.1;

The structure of E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration, PDB code: 3lq4 was solved by W.Furey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.52 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.210, 142.220, 82.850, 90.00, 101.87, 90.00
R / Rfree (%)	19.9 / 23.6

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration (pdb code 3lq4). 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 Complex E1 E235A Mutant with High Tdp Concentration, PDB code: 3lq4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration


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 Complex E1 E235A Mutant with High Tdp Concentration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg888 b:44.9 occ:0.75 OD1 A:ASN260 2.3 43.8 1.0 O A:HOH891 2.3 38.0 1.0 OD1 A:ASP230 2.4 37.8 1.0 O A:GLN262 2.5 61.1 1.0 O12 A:TDP887 2.6 37.5 0.8 O23 A:TDP887 2.8 44.4 0.8 CG A:ASN260 2.9 42.5 1.0 ND2 A:ASN260 3.0 42.0 1.0 CG A:ASP230 3.2 37.6 1.0 P2 A:TDP887 3.5 44.3 0.8 O11 A:TDP887 3.5 41.5 0.8 OD2 A:ASP230 3.6 39.0 1.0 O21 A:TDP887 3.6 44.8 0.8 P1 A:TDP887 3.7 39.3 0.8 C A:GLN262 3.7 62.0 1.0 O A:ASN258 3.8 29.0 1.0 N A:ASP230 3.8 32.4 1.0 O A:HOH912 4.1 59.5 1.0 N A:ASN260 4.2 36.9 1.0 N A:GLN262 4.2 57.0 1.0 CB A:ASN260 4.3 41.2 1.0 N A:GLY231 4.3 33.8 1.0 CB A:ASP230 4.5 35.5 1.0 CA A:GLN262 4.5 60.5 1.0 CA A:GLY229 4.5 30.2 1.0 N A:ARG263 4.6 63.4 1.0 CA A:ARG263 4.6 66.0 1.0 C A:GLY229 4.6 31.7 1.0 O5G A:TDP887 4.6 40.6 0.8 CA A:ASP230 4.6 34.1 1.0 CA A:ASN260 4.6 41.3 1.0 N A:LEU261 4.7 48.0 1.0 C A:ASN260 4.8 44.2 1.0 O13 A:TDP887 4.8 37.9 0.8 C A:ASN258 4.9 31.3 1.0 O A:ARG263 4.9 68.6 1.0 O22 A:TDP887 4.9 45.7 0.8

Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase Complex E1 E235A Mutant with High Tdp Concentration


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 Complex E1 E235A Mutant with High Tdp Concentration within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg888 b:36.4 occ:1.00 OD1 B:ASN260 2.1 26.4 1.0 O B:HOH1061 2.3 29.8 1.0 OD1 B:ASP230 2.3 38.0 1.0 O B:GLN262 2.4 42.1 1.0 O12 B:TDP887 2.5 34.0 1.0 O23 B:TDP887 2.7 39.0 1.0 CG B:ASN260 3.0 32.1 1.0 CG B:ASP230 3.1 37.0 1.0 OD2 B:ASP230 3.4 36.3 1.0 ND2 B:ASN260 3.4 29.1 1.0 C B:GLN262 3.5 44.8 1.0 P2 B:TDP887 3.6 36.8 1.0 P1 B:TDP887 3.6 35.5 1.0 O11 B:TDP887 3.7 36.5 1.0 N B:ASP230 3.8 29.3 1.0 N B:GLN262 3.8 40.5 1.0 O B:ASN258 3.9 31.8 1.0 O21 B:TDP887 4.0 38.9 1.0 N B:GLY231 4.1 31.4 1.0 N B:ASN260 4.1 30.6 1.0 CA B:GLN262 4.2 44.1 1.0 CB B:ASP230 4.3 33.9 1.0 CB B:ASN260 4.4 31.6 1.0 CA B:ASP230 4.5 32.7 1.0 N B:LEU261 4.5 34.0 1.0 N B:ARG263 4.6 47.4 1.0 CA B:ASN260 4.6 32.3 1.0 O5G B:TDP887 4.6 37.9 1.0 C B:ASN260 4.7 33.1 1.0 C B:GLY229 4.7 29.5 1.0 O13 B:TDP887 4.7 35.8 1.0 CA B:GLY229 4.7 28.4 1.0 C B:ASP230 4.8 30.4 1.0 CA B:ARG263 4.8 51.0 1.0 C B:LEU261 4.9 39.6 1.0 O B:ARG263 4.9 52.5 1.0 CG2 B:VAL268 4.9 41.5 1.0 CA B:GLY231 5.0 31.3 1.0 O22 B:TDP887 5.0 40.1 1.0 CB B:GLN262 5.0 47.4 1.0

N.S.Nemeria, P.Arjunan, K.Chandrasekhar, M.Mossad, K.Tittmann, W.Furey, F.Jordan. Communication Between Thiamin Cofactors in the Escherichia Coli Pyruvate Dehydrogenase Complex E1 Component Active Centers: Evidence For A "Direct Pathway" Between the 4'-Aminopyrimidine N1' Atoms. J.Biol.Chem. V. 285 11197 2010.
ISSN: ISSN 0021-9258
PubMed: 20106967
DOI: 10.1074/JBC.M109.069179