Magnesium in PDB 2q5q: X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid

All present enzymatic activity of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid:
4.1.1.43;

The structure of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid, PDB code: 2q5q was solved by W.Versees, S.Spaepen, M.D.Wood, F.J.Leeper, J.Vanderleyden, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	74.688, 145.120, 194.107, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.6

The binding sites of Magnesium atom in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid (pdb code 2q5q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid, PDB code: 2q5q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:23.8 occ:1.00 O A:HOH5009 2.0 23.8 1.0 O22 A:TPW2002 2.0 26.7 1.0 O13 A:TPW2002 2.0 24.9 1.0 OD1 A:ASP429 2.1 21.4 1.0 OD1 A:ASN456 2.1 26.0 1.0 O A:SER458 2.1 21.9 1.0 CG A:ASN456 3.1 31.2 1.0 CG A:ASP429 3.2 21.4 1.0 P1 A:TPW2002 3.2 23.9 1.0 P2 A:TPW2002 3.2 24.7 1.0 C A:SER458 3.3 20.7 1.0 O11 A:TPW2002 3.4 26.1 1.0 ND2 A:ASN456 3.4 27.6 1.0 OD2 A:ASP429 3.6 23.8 1.0 O5G A:TPW2002 3.8 24.2 1.0 N A:ASP429 3.9 23.9 1.0 N A:SER458 4.0 23.6 1.0 N A:GLU460 4.2 26.1 1.0 O A:PHE454 4.2 23.1 1.0 O23 A:TPW2002 4.2 29.4 1.0 CA A:SER458 4.2 21.1 1.0 N A:GLY430 4.2 22.2 1.0 O21 A:TPW2002 4.3 21.1 1.0 N A:TRP459 4.3 20.6 1.0 N A:ASN456 4.3 25.8 1.0 O12 A:TPW2002 4.4 21.0 1.0 CB A:ASP429 4.4 22.4 1.0 CB A:ASN456 4.4 26.8 1.0 O A:HOH5198 4.5 28.1 1.0 CA A:TRP459 4.5 22.2 1.0 CA A:ASP429 4.6 23.5 1.0 CB A:GLU460 4.7 29.4 1.0 CA A:GLY428 4.7 22.4 1.0 CB A:SER458 4.7 22.1 1.0 C A:GLY428 4.7 23.6 1.0 CA A:ASN456 4.8 27.7 1.0 C A:ASN456 4.8 25.2 1.0 C A:TRP459 4.9 22.7 1.0 N A:ALA457 4.9 26.2 1.0 C A:ASP429 5.0 23.4 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and 5-Phenyl-2-Oxo-Valeric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4001 b:20.1 occ:1.00 O22 B:TPW2001 2.0 21.1 1.0 O13 B:TPW2001 2.0 19.1 1.0 OD1 B:ASP429 2.1 20.6 1.0 O B:SER458 2.1 15.9 1.0 O B:HOH5007 2.1 17.2 1.0 OD1 B:ASN456 2.2 16.8 1.0 CG B:ASN456 3.1 21.4 1.0 CG B:ASP429 3.2 20.8 1.0 P1 B:TPW2001 3.2 19.0 1.0 P2 B:TPW2001 3.2 17.9 1.0 C B:SER458 3.3 16.8 1.0 O11 B:TPW2001 3.4 18.6 1.0 ND2 B:ASN456 3.5 16.9 1.0 OD2 B:ASP429 3.7 20.8 1.0 O5G B:TPW2001 3.8 19.0 1.0 N B:ASP429 4.0 18.4 1.0 N B:SER458 4.0 19.5 1.0 N B:GLU460 4.1 18.0 1.0 CA B:SER458 4.1 19.2 1.0 O23 B:TPW2001 4.2 22.2 1.0 N B:GLY430 4.3 18.1 1.0 N B:TRP459 4.3 17.7 1.0 N B:ASN456 4.3 20.4 1.0 O21 B:TPW2001 4.3 20.6 1.0 O B:PHE454 4.3 23.0 1.0 O12 B:TPW2001 4.4 14.8 1.0 O B:HOH5199 4.4 21.9 1.0 CB B:ASP429 4.4 16.9 1.0 CA B:TRP459 4.5 16.5 1.0 CB B:ASN456 4.5 18.7 1.0 CB B:GLU460 4.6 19.7 1.0 CB B:SER458 4.6 21.0 1.0 CA B:ASP429 4.7 18.2 1.0 CA B:GLY428 4.8 16.6 1.0 C B:GLY428 4.8 17.8 1.0 CA B:ASN456 4.8 19.5 1.0 C B:TRP459 4.9 18.1 1.0 C B:ASN456 4.9 17.4 1.0 N B:ALA457 4.9 18.6 1.0 C B:ASP429 5.0 18.6 1.0

W.Versees, S.Spaepen, M.D.Wood, F.J.Leeper, J.Vanderleyden, J.Steyaert. Molecular Mechanism of Allosteric Substrate Activation in A Thiamine Diphosphate-Dependent Decarboxylase. J.Biol.Chem. V. 282 35269 2007.
ISSN: ISSN 0021-9258
PubMed: 17905741
DOI: 10.1074/JBC.M706048200