Magnesium in PDB 4kgd: High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate

All present enzymatic activity of High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate:
1.2.3.3;

The structure of High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate, PDB code: 4kgd was solved by P.Neumann, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.06
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.280, 154.160, 165.470, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.1

The structure of High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate (pdb code 4kgd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate, PDB code: 4kgd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:5.9 occ:1.00 O12 A:TDP704 2.0 5.8 1.0 O A:GLN476 2.0 5.9 1.0 OD1 A:ASP447 2.0 6.9 1.0 O A:HOH803 2.1 6.2 1.0 O21 A:TDP704 2.1 5.5 1.0 OD1 A:ASN474 2.1 6.5 1.0 CG A:ASN474 3.1 6.5 1.0 P1 A:TDP704 3.2 5.5 1.0 CG A:ASP447 3.2 5.7 1.0 P2 A:TDP704 3.2 5.5 1.0 C A:GLN476 3.3 5.7 1.0 ND2 A:ASN474 3.4 7.8 1.0 O11 A:TDP704 3.4 5.3 1.0 O23 A:TDP704 3.8 6.0 1.0 OD2 A:ASP447 3.9 8.3 1.0 N A:GLN476 3.9 5.9 1.0 N A:ASP447 3.9 5.9 1.0 O5G A:TDP704 4.0 5.9 1.0 N A:GLY448 4.1 5.7 1.0 CA A:GLN476 4.1 6.2 1.0 N A:GLY478 4.2 6.3 1.0 O A:PHE472 4.2 7.3 1.0 N A:TYR477 4.2 6.0 1.0 O13 A:TDP704 4.4 6.2 1.0 CA A:TYR477 4.4 5.7 1.0 CB A:ASP447 4.4 6.4 1.0 N A:ASN474 4.4 6.9 1.0 CB A:ASN474 4.5 7.0 1.0 O22 A:TDP704 4.5 5.2 1.0 CZ A:PHE497 4.5 10.0 1.0 CA A:ASP447 4.6 5.9 1.0 CB A:GLN476 4.6 7.4 1.0 C A:GLY446 4.7 5.7 1.0 CA A:GLY446 4.8 6.0 1.0 N A:CYS475 4.8 6.7 1.0 C A:ASP447 4.8 6.1 1.0 C A:TYR477 4.8 5.9 1.0 CA A:ASN474 4.8 7.2 1.0 C A:ASN474 5.0 6.9 1.0

Magnesium binding site 2 out of 2 in the High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Crystal Structure of Pyruvate Oxidase From L. Plantarum in Complex with Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:5.4 occ:1.00 O12 B:TDP703 2.0 5.1 0.9 O B:GLN476 2.1 5.6 1.0 OD1 B:ASP447 2.1 6.1 1.0 O21 B:TDP703 2.1 5.1 0.9 OD1 B:ASN474 2.1 5.8 1.0 O B:HOH802 2.1 6.0 1.0 CG B:ASN474 3.1 5.7 1.0 P1 B:TDP703 3.2 4.9 0.9 C B:GLN476 3.2 5.4 1.0 P2 B:TDP703 3.3 4.8 0.9 CG B:ASP447 3.3 5.7 1.0 ND2 B:ASN474 3.4 7.2 1.0 O11 B:TDP703 3.4 4.7 0.9 O22 B:TDP703 3.7 5.0 0.9 OD2 B:ASP447 3.9 7.7 1.0 N B:GLN476 3.9 5.2 1.0 N B:ASP447 3.9 5.4 1.0 O5G B:TDP703 4.0 5.3 0.9 N B:GLY448 4.1 5.7 1.0 CA B:GLN476 4.1 5.2 1.0 N B:GLY478 4.2 4.9 1.0 O B:PHE472 4.2 7.1 1.0 N B:TYR477 4.2 5.3 1.0 CA B:TYR477 4.4 5.4 1.0 CB B:ASP447 4.4 5.7 1.0 O13 B:TDP703 4.4 5.5 0.9 CB B:ASN474 4.5 6.2 1.0 N B:ASN474 4.5 6.3 1.0 O23 B:TDP703 4.5 5.1 0.9 CA B:ASP447 4.5 5.8 1.0 CB B:GLN476 4.6 6.5 1.0 CZ B:PHE497 4.6 9.5 1.0 CA B:GLY446 4.7 5.4 1.0 C B:GLY446 4.7 5.3 1.0 N B:CYS475 4.8 6.2 1.0 C B:ASP447 4.8 5.4 1.0 C B:TYR477 4.8 5.3 1.0 CA B:ASN474 4.8 6.6 1.0 C B:ASN474 5.0 6.5 1.0 CA B:GLY448 5.0 6.0 1.0

D.Meyer, P.Neumann, R.Ficner, K.Tittmann. Observation of A Stable Carbene at the Active Site of A Thiamin Enzyme. Nat.Chem.Biol. V. 9 488 2013.
ISSN: ISSN 1552-4450
PubMed: 23748673
DOI: 10.1038/NCHEMBIO.1275