Magnesium in PDB 1l8a: E. Coli Pyruvate Dehydrogenase

All present enzymatic activity of E. Coli Pyruvate Dehydrogenase:
1.2.4.1;

The structure of E. Coli Pyruvate Dehydrogenase, PDB code: 1l8a was solved by W.Furey, P.Arjunan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.690, 141.600, 82.460, 90.00, 102.40, 90.00
R / Rfree (%)	18.9 / 23.6

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase (pdb code 1l8a). 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, PDB code: 1l8a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg888 b:13.2 occ:1.00 OD1 B:ASP230 2.1 9.8 1.0 OD1 B:ASN260 2.1 10.3 1.0 O B:GLN262 2.2 12.6 1.0 O B:HOH903 2.3 12.3 1.0 O12 A:TDP887 2.4 10.9 1.0 O23 A:TDP887 2.5 11.1 1.0 CG B:ASN260 3.1 10.6 1.0 CG B:ASP230 3.1 10.0 1.0 C B:GLN262 3.3 15.7 1.0 ND2 B:ASN260 3.4 9.8 1.0 P2 A:TDP887 3.5 11.6 1.0 P1 A:TDP887 3.6 10.1 1.0 OD2 B:ASP230 3.6 12.2 1.0 O11 A:TDP887 3.6 11.0 1.0 N B:GLN262 3.8 13.6 1.0 N B:ASP230 3.9 8.8 1.0 O21 A:TDP887 4.0 11.9 1.0 N B:GLY231 4.0 10.4 1.0 O B:ASN258 4.0 10.1 1.0 CA B:GLN262 4.1 16.3 1.0 N B:ARG263 4.2 14.8 1.0 CB B:ASP230 4.4 8.7 1.0 CA B:ARG263 4.4 14.9 1.0 O5G A:TDP887 4.4 11.5 1.0 N B:ASN260 4.4 9.8 1.0 CB B:ASN260 4.4 9.5 1.0 CA B:ASP230 4.5 8.7 1.0 N B:LEU261 4.6 9.4 1.0 O13 A:TDP887 4.7 10.1 1.0 C B:ASN260 4.8 10.0 1.0 C B:ASP230 4.8 7.8 1.0 CA B:ASN260 4.8 9.6 1.0 NZ B:LYS392 4.8 30.3 1.0 C B:GLY229 4.8 9.9 1.0 C B:LEU261 4.8 12.4 1.0 O22 A:TDP887 4.8 14.5 1.0 CB B:GLN262 4.9 22.8 1.0 CG2 B:VAL268 4.9 14.4 1.0 CA B:GLY229 4.9 8.6 1.0 CE B:LYS392 4.9 32.3 1.0 CA B:GLY231 4.9 8.9 1.0

Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg888 b:13.2 occ:1.00 OD1 A:ASN260 2.1 8.6 1.0 OD2 A:ASP230 2.2 14.4 1.0 O A:GLN262 2.3 15.2 1.0 O A:HOH909 2.3 8.0 1.0 O23 B:TDP887 2.5 16.0 1.0 O12 B:TDP887 2.5 14.1 1.0 CG A:ASN260 3.0 12.0 1.0 CG A:ASP230 3.2 15.6 1.0 ND2 A:ASN260 3.4 10.2 1.0 C A:GLN262 3.4 18.4 1.0 P2 B:TDP887 3.5 16.7 1.0 OD1 A:ASP230 3.6 11.2 1.0 O11 B:TDP887 3.6 13.4 1.0 P1 B:TDP887 3.6 13.3 1.0 O A:ASN258 3.8 10.2 1.0 N A:ASP230 3.8 8.2 1.0 O21 B:TDP887 3.9 16.1 1.0 N A:GLN262 3.9 17.2 1.0 N A:GLY231 4.1 9.1 1.0 CA A:GLN262 4.2 20.1 1.0 N A:ASN260 4.2 11.4 1.0 CB A:ASN260 4.4 10.7 1.0 CB A:ASP230 4.4 11.2 1.0 O5G B:TDP887 4.4 15.7 1.0 N A:ARG263 4.5 16.9 1.0 N A:LEU261 4.5 11.5 1.0 CA A:ASP230 4.5 8.9 1.0 CA A:ARG263 4.6 16.4 1.0 CA A:ASN260 4.7 12.4 1.0 C A:GLY229 4.7 8.4 1.0 CA A:GLY229 4.7 7.6 1.0 CD A:LYS392 4.7 33.7 1.0 C A:ASN260 4.7 12.2 1.0 O13 B:TDP887 4.8 11.8 1.0 O22 B:TDP887 4.8 17.6 1.0 C A:ASP230 4.9 9.2 1.0 C A:LEU261 4.9 16.0 1.0 CB A:GLN262 5.0 23.7 1.0

P.Arjunan, N.Nemeria, A.Brunskill, K.Chandrasekhar, M.Sax, Y.Yan, F.Jordan, J.R.Guest, W.Furey. Structure of the Pyruvate Dehydrogenase Multienzyme Complex E1 Component From Escherichia Coli at 1.85 A Resolution. Biochemistry V. 41 5213 2002.
ISSN: ISSN 0006-2960
PubMed: 11955070
DOI: 10.1021/BI0118557