Magnesium in PDB 6haf: Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate

The structure of Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate, PDB code: 6haf was solved by L.M.Funk, V.Sautner, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.36 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.180, 154.350, 165.520, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 15.6

The structure of Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate (pdb code 6haf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate, PDB code: 6haf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Oxidase Variant E59Q 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 Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:8.5 occ:1.00 OD1 A:ASP447 2.0 8.9 1.0 O12 A:TDP704 2.0 8.0 1.0 O A:GLN476 2.0 8.5 1.0 O A:HOH868 2.1 8.3 1.0 O21 A:TDP704 2.1 9.0 1.0 OD1 A:ASN474 2.2 9.0 1.0 HD21 A:ASN474 3.0 11.0 1.0 CG A:ASN474 3.1 9.0 1.0 H A:GLN476 3.2 10.1 1.0 CG A:ASP447 3.2 9.1 1.0 P1 A:TDP704 3.2 7.9 1.0 P2 A:TDP704 3.2 8.4 1.0 C A:GLN476 3.2 8.7 1.0 H A:GLY448 3.3 10.0 1.0 H A:ASP447 3.3 10.3 1.0 H A:GLY478 3.3 10.4 1.0 ND2 A:ASN474 3.4 9.1 1.0 O11 A:TDP704 3.4 7.8 1.0 H A:ASN474 3.7 11.3 1.0 HA A:TYR477 3.7 10.0 1.0 HZ A:PHE497 3.8 13.8 1.0 O23 A:TDP704 3.8 8.2 1.0 OD2 A:ASP447 3.9 10.1 1.0 N A:GLN476 3.9 8.4 1.0 N A:ASP447 4.0 8.6 1.0 HB2 A:GLN476 4.0 11.9 1.0 O5G A:TDP704 4.1 8.0 1.0 CA A:GLN476 4.1 8.6 1.0 N A:GLY448 4.1 8.4 1.0 N A:GLY478 4.2 8.6 1.0 HA3 A:GLY446 4.2 9.8 1.0 N A:TYR477 4.2 8.8 1.0 O A:PHE472 4.2 9.5 1.0 HD22 A:ASN474 4.2 11.0 1.0 CA A:TYR477 4.3 8.3 1.0 O13 A:TDP704 4.4 8.3 1.0 CB A:ASP447 4.4 8.0 1.0 N A:ASN474 4.5 9.4 1.0 CB A:ASN474 4.5 9.5 1.0 CA A:ASP447 4.6 8.6 1.0 CZ A:PHE497 4.6 11.5 1.0 CB A:GLN476 4.6 9.9 1.0 O22 A:TDP704 4.6 8.3 1.0 H A:CYS475 4.6 11.0 1.0 HA2 A:GLY446 4.7 9.8 1.0 HA3 A:GLY448 4.7 10.2 1.0 C A:GLY446 4.7 8.4 1.0 CA A:GLY446 4.8 8.1 1.0 N A:CYS475 4.8 9.2 1.0 C A:TYR477 4.8 8.6 1.0 HD1 A:TYR477 4.8 10.0 1.0 C A:ASP447 4.8 8.8 1.0 CA A:ASN474 4.8 9.5 1.0 HA A:THR473 4.9 11.0 1.0 HA3 A:GLY478 4.9 10.4 1.0 HB3 A:ASP447 4.9 9.6 1.0 HA A:GLN476 4.9 10.4 1.0 HB2 A:ASN474 5.0 11.4 1.0 HB3 A:ASN474 5.0 11.4 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Oxidase Variant E59Q 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 Pyruvate Oxidase Variant E59Q From L. Plantarum in Complex with Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:8.0 occ:1.00 O12 B:TDP704 2.0 8.3 1.0 O B:GLN476 2.0 8.0 1.0 OD1 B:ASP447 2.1 7.8 1.0 O21 B:TDP704 2.1 7.9 1.0 O B:HOH862 2.1 7.9 1.0 OD1 B:ASN474 2.1 8.0 1.0 HD21 B:ASN474 3.0 11.1 1.0 CG B:ASN474 3.1 8.0 1.0 H B:GLN476 3.2 9.7 1.0 P1 B:TDP704 3.2 7.8 1.0 CG B:ASP447 3.2 8.5 1.0 P2 B:TDP704 3.2 7.7 1.0 C B:GLN476 3.2 7.4 1.0 H B:GLY448 3.3 9.9 1.0 H B:ASP447 3.3 9.3 1.0 ND2 B:ASN474 3.4 9.2 1.0 H B:GLY478 3.4 8.3 1.0 O11 B:TDP704 3.4 7.7 1.0 H B:ASN474 3.6 10.1 1.0 HA B:TYR477 3.7 8.8 1.0 O22 B:TDP704 3.8 7.7 1.0 HZ B:PHE497 3.8 12.7 1.0 OD2 B:ASP447 3.9 9.8 1.0 N B:GLN476 3.9 8.1 1.0 N B:ASP447 3.9 7.7 1.0 HB2 B:GLN476 4.0 11.1 1.0 O5G B:TDP704 4.1 7.3 1.0 CA B:GLN476 4.1 7.5 1.0 N B:GLY448 4.1 8.2 1.0 O B:PHE472 4.2 9.0 1.0 HA3 B:GLY446 4.2 8.3 1.0 N B:GLY478 4.2 6.9 1.0 HD22 B:ASN474 4.2 11.1 1.0 N B:TYR477 4.2 7.2 1.0 O13 B:TDP704 4.4 7.7 1.0 CA B:TYR477 4.4 7.3 1.0 CB B:ASP447 4.4 8.5 1.0 N B:ASN474 4.4 8.4 1.0 CB B:ASN474 4.4 8.3 1.0 CA B:ASP447 4.5 8.1 1.0 O23 B:TDP704 4.5 8.0 1.0 H B:CYS475 4.6 10.4 1.0 CB B:GLN476 4.6 9.2 1.0 HA2 B:GLY446 4.6 8.3 1.0 CZ B:PHE497 4.6 10.6 1.0 C B:GLY446 4.7 7.6 1.0 CA B:GLY446 4.7 6.9 1.0 HA3 B:GLY448 4.7 9.9 1.0 N B:CYS475 4.8 8.6 1.0 HD1 B:TYR477 4.8 9.8 1.0 C B:ASP447 4.8 7.9 1.0 CA B:ASN474 4.8 8.4 1.0 C B:TYR477 4.9 7.6 1.0 HA B:THR473 4.9 10.4 1.0 HB3 B:ASP447 4.9 10.2 1.0 HA3 B:GLY478 4.9 9.7 1.0 HB3 B:ASN474 4.9 10.0 1.0 HA B:GLN476 4.9 9.0 1.0 HB2 B:ASN474 5.0 10.0 1.0 C B:ASN474 5.0 8.5 1.0

S.Dai, L.M.Funk, F.R.Von Pappenheim, V.Sautner, M.Paulikat, B.Schroder, J.Uranga, R.A.Mata, K.Tittmann. Low-Barrier Hydrogen Bonds in Enzyme Cooperativity. Nature V. 573 609 2019.
ISSN: ESSN 1476-4687
PubMed: 31534226
DOI: 10.1038/S41586-019-1581-9