Magnesium in PDB 2q5o: X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and Phenylpyruvate

All present enzymatic activity of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and Phenylpyruvate:
4.1.1.43;

The structure of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and Phenylpyruvate, PDB code: 2q5o 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)	28.10 / 2.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	74.896, 145.584, 194.042, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24

The binding sites of Magnesium atom in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp and Phenylpyruvate (pdb code 2q5o). 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 Phenylpyruvate, PDB code: 2q5o:
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 Phenylpyruvate


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 Phenylpyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:33.1 occ:1.00 O22 A:TPW2002 1.9 44.0 1.0 O A:SER458 2.0 35.1 1.0 O13 A:TPW2002 2.1 42.0 1.0 OD1 A:ASN456 2.1 42.0 1.0 O A:HOH5285 2.2 28.1 1.0 OD1 A:ASP429 2.2 34.7 1.0 CG A:ASN456 3.0 45.5 1.0 P2 A:TPW2002 3.1 43.2 1.0 P1 A:TPW2002 3.1 40.2 1.0 C A:SER458 3.2 33.5 1.0 CG A:ASP429 3.2 39.0 1.0 O11 A:TPW2002 3.3 45.0 1.0 ND2 A:ASN456 3.3 40.7 1.0 OD2 A:ASP429 3.5 41.9 1.0 O5G A:TPW2002 3.5 35.2 1.0 N A:SER458 4.0 39.5 1.0 N A:GLU460 4.0 39.3 1.0 CA A:SER458 4.1 35.5 1.0 O21 A:TPW2002 4.1 40.6 1.0 N A:ASP429 4.1 35.9 1.0 O23 A:TPW2002 4.1 48.9 1.0 N A:TRP459 4.2 31.6 1.0 CA A:TRP459 4.3 34.8 1.0 O A:PHE454 4.4 36.8 1.0 N A:GLY430 4.4 35.8 1.0 O12 A:TPW2002 4.4 39.9 1.0 CB A:ASN456 4.5 41.3 1.0 CB A:GLU460 4.5 39.5 1.0 N A:ASN456 4.5 38.9 1.0 CB A:ASP429 4.5 36.5 1.0 CB A:SER458 4.6 39.3 1.0 C A:TRP459 4.7 33.5 1.0 CA A:ASP429 4.8 38.0 1.0 CA A:GLY428 4.8 36.0 1.0 C A:ASN456 4.9 40.4 1.0 CA A:ASN456 4.9 42.0 1.0 C A:GLY428 4.9 38.1 1.0 CA A:GLU460 4.9 40.5 1.0 OG A:SER458 4.9 33.6 1.0 C5B A:TPW2002 4.9 33.2 1.0 N A:ALA457 5.0 42.7 1.0

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


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 Phenylpyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4001 b:32.3 occ:1.00 O B:HOH5290 1.9 28.4 1.0 O22 B:TPW2001 1.9 35.1 1.0 O13 B:TPW2001 2.1 33.9 1.0 O B:SER458 2.1 23.5 1.0 OD1 B:ASN456 2.1 28.9 1.0 OD1 B:ASP429 2.2 31.4 1.0 CG B:ASN456 3.0 32.6 1.0 P2 B:TPW2001 3.1 29.0 1.0 P1 B:TPW2001 3.2 29.7 1.0 C B:SER458 3.3 29.0 1.0 CG B:ASP429 3.3 32.4 1.0 ND2 B:ASN456 3.4 26.8 1.0 O11 B:TPW2001 3.4 32.5 1.0 O5G B:TPW2001 3.8 34.9 1.0 OD2 B:ASP429 3.8 26.0 1.0 N B:SER458 4.0 32.6 1.0 O23 B:TPW2001 4.0 29.4 1.0 N B:ASP429 4.0 24.3 1.0 O B:HOH5109 4.1 40.1 1.0 N B:GLU460 4.1 27.5 1.0 CA B:SER458 4.1 32.7 1.0 N B:TRP459 4.2 29.3 1.0 O B:PHE454 4.3 32.4 1.0 O21 B:TPW2001 4.3 29.7 1.0 N B:ASN456 4.3 31.7 1.0 N B:GLY430 4.4 29.1 1.0 O12 B:TPW2001 4.4 31.4 1.0 CA B:TRP459 4.4 28.8 1.0 CB B:ASN456 4.4 30.2 1.0 CB B:SER458 4.6 36.1 1.0 CB B:ASP429 4.6 29.9 1.0 CB B:GLU460 4.6 24.9 1.0 CA B:GLY428 4.7 25.6 1.0 CA B:ASP429 4.8 29.0 1.0 CA B:ASN456 4.8 28.1 1.0 C B:GLY428 4.8 26.2 1.0 C B:TRP459 4.8 30.9 1.0 OG B:SER458 4.9 37.0 1.0 C B:ASN456 4.9 27.5 1.0 N B:ALA457 4.9 25.1 1.0 CA B:GLU460 5.0 32.1 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