Magnesium in PDB 1rp7: E. Coli Pyruvate Dehydrogenase Inhibitor Complex

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

The structure of E. Coli Pyruvate Dehydrogenase Inhibitor Complex, PDB code: 1rp7 was solved by P.Arjunan, K.Chandrasekhar, W.Furey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.550, 141.840, 82.170, 90.00, 102.61, 90.00
R / Rfree (%)	19.2 / 25.2

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase Inhibitor Complex (pdb code 1rp7). 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 Inhibitor Complex, PDB code: 1rp7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase Inhibitor 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 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg890 b:16.7 occ:1.00 O A:GLN262 2.2 10.8 1.0 OD1 A:ASP230 2.2 17.4 1.0 OD1 A:ASN260 2.3 16.6 1.0 O23 A:TZD889 2.3 13.9 1.0 O A:HOH1113 2.3 10.7 1.0 O12 A:TZD889 2.3 14.3 1.0 CG A:ASN260 3.2 13.3 1.0 P2 A:TZD889 3.2 15.4 1.0 CG A:ASP230 3.3 17.2 1.0 O11 A:TZD889 3.3 14.5 1.0 C A:GLN262 3.4 16.7 1.0 P1 A:TZD889 3.4 12.2 1.0 ND2 A:ASN260 3.5 11.2 1.0 O21 A:TZD889 3.6 15.4 1.0 OD2 A:ASP230 3.8 17.7 1.0 N A:ASP230 3.9 6.2 1.0 N A:GLN262 4.0 17.0 1.0 O A:ASN258 4.1 9.6 1.0 N A:GLY231 4.2 10.5 1.0 O5G A:TZD889 4.2 14.9 1.0 CA A:GLN262 4.2 18.3 1.0 N A:ARG263 4.3 17.6 1.0 CA A:ARG263 4.4 18.9 1.0 N A:ASN260 4.4 14.2 1.0 CB A:ASN260 4.5 12.9 1.0 CB A:ASP230 4.6 11.5 1.0 O13 A:TZD889 4.6 14.4 1.0 O22 A:TZD889 4.6 16.7 1.0 CA A:ASP230 4.6 9.7 1.0 NZ A:LYS392 4.7 21.6 1.0 N A:LEU261 4.7 16.7 1.0 CA A:GLY229 4.7 7.1 1.0 C A:GLY229 4.7 9.5 1.0 C A:ASN260 4.8 15.8 1.0 CA A:ASN260 4.8 16.6 1.0 CE A:LYS392 4.9 23.2 1.0 C A:ASP230 4.9 10.0 1.0 C A:LEU261 5.0 17.4 1.0

Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase Inhibitor 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 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg888 b:16.4 occ:1.00 O B:GLN262 2.1 15.4 1.0 OD1 B:ASN260 2.2 15.7 1.0 OD1 B:ASP230 2.2 15.5 1.0 O B:HOH889 2.3 14.4 1.0 O12 B:TZD887 2.4 14.2 1.0 O23 B:TZD887 2.4 17.0 1.0 CG B:ASN260 3.2 16.4 1.0 C B:GLN262 3.2 17.0 1.0 CG B:ASP230 3.2 14.5 1.0 ND2 B:ASN260 3.6 12.2 1.0 N B:GLN262 3.6 14.7 1.0 P2 B:TZD887 3.6 12.4 1.0 OD2 B:ASP230 3.6 14.0 1.0 P1 B:TZD887 3.6 11.4 1.0 O11 B:TZD887 3.8 12.3 1.0 CA B:GLN262 3.9 18.7 1.0 N B:ASP230 4.1 10.6 1.0 O B:ASN258 4.1 9.4 1.0 O21 B:TZD887 4.1 12.9 1.0 N B:ARG263 4.2 17.7 1.0 N B:GLY231 4.2 9.8 1.0 O5G B:TZD887 4.4 10.5 1.0 N B:ASN260 4.4 12.3 1.0 CA B:ARG263 4.5 18.6 1.0 N B:LEU261 4.5 16.2 1.0 CB B:ASN260 4.5 15.9 1.0 CB B:ASP230 4.5 13.5 1.0 NZ B:LYS392 4.5 25.1 1.0 C B:LEU261 4.7 14.1 1.0 CD B:LYS392 4.7 22.9 1.0 C B:ASN260 4.7 16.1 1.0 CA B:ASP230 4.7 11.2 1.0 CG2 B:VAL268 4.8 7.0 1.0 CG B:GLN262 4.8 30.9 1.0 O13 B:TZD887 4.8 12.1 1.0 CA B:ASN260 4.8 15.4 1.0 CB B:GLN262 4.9 24.1 1.0 O22 B:TZD887 4.9 16.0 1.0 O B:ARG263 4.9 21.4 1.0 C B:ASP230 5.0 9.9 1.0 C B:GLY229 5.0 11.8 1.0

P.Arjunan, K.Chandrasekhar, M.Sax, A.Brunskill, N.Nemeria, F.Jordan, W.Furey. Structural Determinants of Enzyme Binding Affinity: the E1 Component of Pyruvate Dehydrogenase From Escherichia Coli in Complex with the Inhibitor Thiamin Thiazolone Diphosphate. Biochemistry V. 43 2405 2004.
ISSN: ISSN 0006-2960
PubMed: 14992577
DOI: 10.1021/BI030200Y