Magnesium in PDB 2q5j: X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp

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

The structure of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp, PDB code: 2q5j 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)	50.00 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.541, 179.809, 121.030, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 28.9

The binding sites of Magnesium atom in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 3- Deaza-Thdp (pdb code 2q5j). 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, PDB code: 2q5j:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:50.8 occ:1.00 OD1 A:ASP429 2.0 18.4 1.0 O22 A:TPW1002 2.0 33.3 1.0 OD1 A:ASN456 2.1 43.8 1.0 O13 A:TPW1002 2.2 28.3 1.0 O A:SER458 2.2 25.5 1.0 CG A:ASP429 2.9 20.6 1.0 CG A:ASN456 3.0 37.6 1.0 P2 A:TPW1002 3.3 36.6 1.0 P1 A:TPW1002 3.3 40.7 1.0 OD2 A:ASP429 3.4 17.3 1.0 ND2 A:ASN456 3.4 19.4 1.0 C A:SER458 3.5 22.9 1.0 O11 A:TPW1002 3.6 41.0 1.0 O5G A:TPW1002 3.8 17.7 1.0 N A:ASP429 3.8 23.7 1.0 N A:GLY430 3.8 18.4 1.0 O A:PHE454 4.0 25.0 1.0 N A:SER458 4.0 24.2 1.0 CB A:ASP429 4.2 22.0 1.0 O21 A:TPW1002 4.2 23.7 1.0 N A:ASN456 4.3 48.6 1.0 CA A:SER458 4.3 17.5 1.0 N A:GLU460 4.3 24.8 1.0 O23 A:TPW1002 4.4 20.3 1.0 N A:TRP459 4.4 31.0 1.0 CA A:ASP429 4.4 23.6 1.0 CB A:ASN456 4.4 22.0 1.0 CA A:TRP459 4.5 34.2 1.0 O12 A:TPW1002 4.6 34.0 1.0 C A:GLY428 4.6 19.0 1.0 C A:ASP429 4.7 27.6 1.0 CA A:GLY428 4.7 24.5 1.0 N A:ALA457 4.7 28.3 1.0 CA A:GLY430 4.7 38.8 1.0 OG A:SER458 4.8 14.0 1.0 CA A:ASN456 4.8 37.4 1.0 CB A:GLU460 4.9 40.9 1.0 C A:ASN456 4.9 38.0 1.0 C A:TRP459 5.0 25.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:22.2 occ:1.00 OD1 B:ASP429 1.8 39.9 1.0 O22 B:TPW1001 2.1 39.8 1.0 O13 B:TPW1001 2.2 38.2 1.0 OD1 B:ASN456 2.5 28.4 1.0 ND2 B:ASN456 2.6 28.8 1.0 CG B:ASN456 2.8 37.1 1.0 O B:SER458 2.8 25.3 1.0 CG B:ASP429 2.9 27.4 1.0 P2 B:TPW1001 3.1 38.0 1.0 O11 B:TPW1001 3.2 44.0 1.0 P1 B:TPW1001 3.2 50.5 1.0 O B:PHE454 3.4 40.2 1.0 OD2 B:ASP429 3.4 24.5 1.0 N B:ASP429 3.7 24.5 1.0 O23 B:TPW1001 3.8 47.7 1.0 N B:ASN456 3.9 30.9 1.0 O5G B:TPW1001 4.0 48.7 1.0 C B:SER458 4.1 34.3 1.0 CB B:ASN456 4.1 39.2 1.0 O B:HOH2026 4.1 15.6 1.0 CA B:GLY428 4.2 29.1 1.0 N B:GLY430 4.2 30.2 1.0 CB B:ASP429 4.2 32.9 1.0 C B:GLY428 4.3 28.4 1.0 O21 B:TPW1001 4.4 23.4 1.0 CA B:ASP429 4.4 15.7 1.0 O12 B:TPW1001 4.4 37.5 1.0 CA B:ASN456 4.5 32.8 1.0 N B:SER458 4.5 38.3 1.0 C B:PHE454 4.5 39.2 1.0 N B:GLU460 4.7 36.8 1.0 N B:ALA457 4.8 28.8 1.0 C B:ASP429 4.8 20.3 1.0 C B:ASN456 4.9 36.5 1.0 C B:ASN455 4.9 33.6 1.0 CA B:SER458 4.9 33.0 1.0 CA B:ASN455 4.9 43.5 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