Magnesium in PDB 1y9d: Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum

All present enzymatic activity of Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum:
1.2.3.3;

The structure of Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum, PDB code: 1y9d was solved by G.Wille, M.Ritter, M.S.Weiss, S.Konig, W.Mantele, G.Hubner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.30 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.660, 155.780, 100.750, 90.00, 92.92, 90.00
R / Rfree (%)	17.8 / 23.8

The structure of Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum (pdb code 1y9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum, PDB code: 1y9d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum


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 V265A From Lactobacillus Plantarum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2601 b:38.6 occ:1.00 O1A A:TPP2602 1.9 32.0 1.0 O A:GLN476 2.0 34.4 1.0 OD1 A:ASP447 2.2 35.1 1.0 OD1 A:ASN474 2.2 38.1 1.0 O3B A:TPP2602 2.3 30.6 1.0 PA A:TPP2602 3.2 34.4 1.0 CG A:ASN474 3.2 39.0 1.0 C A:GLN476 3.2 35.1 1.0 PB A:TPP2602 3.3 35.3 1.0 CG A:ASP447 3.4 35.0 1.0 O3A A:TPP2602 3.5 32.0 1.0 ND2 A:ASN474 3.5 35.1 1.0 N A:GLN476 3.9 35.1 1.0 OD2 A:ASP447 3.9 37.0 1.0 O2B A:TPP2602 4.0 34.7 1.0 N A:ASP447 4.0 32.2 1.0 O7 A:TPP2602 4.1 32.8 1.0 N A:GLY478 4.1 35.4 1.0 CA A:GLN476 4.1 35.8 1.0 N A:GLY448 4.1 33.5 1.0 N A:TYR477 4.2 34.1 1.0 O2A A:TPP2602 4.3 28.7 1.0 CA A:TYR477 4.4 34.9 1.0 O A:PHE472 4.4 35.4 1.0 N A:ASN474 4.5 37.9 1.0 O1B A:TPP2602 4.5 34.5 1.0 CB A:GLN476 4.5 36.1 1.0 CZ A:PHE497 4.6 40.0 1.0 CB A:ASP447 4.6 32.8 1.0 CB A:ASN474 4.6 37.5 1.0 CA A:ASP447 4.7 32.9 1.0 C A:TYR477 4.8 34.6 1.0 CA A:GLY446 4.8 32.3 1.0 N A:CYS475 4.8 38.6 1.0 C A:GLY446 4.8 32.1 1.0 CA A:ASN474 4.9 37.8 1.0 C A:ASP447 4.9 33.5 1.0 CA A:GLY478 5.0 35.7 1.0 CA A:GLY448 5.0 32.9 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum


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 V265A From Lactobacillus Plantarum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2701 b:31.5 occ:1.00 O B:GLN476 2.0 29.5 1.0 O1A B:TPP2702 2.1 31.5 1.0 OD1 B:ASP447 2.2 24.6 1.0 OD1 B:ASN474 2.2 30.7 1.0 O3B B:TPP2702 2.2 30.8 1.0 CG B:ASN474 3.1 31.3 1.0 PA B:TPP2702 3.2 28.9 1.0 PB B:TPP2702 3.2 31.2 1.0 C B:GLN476 3.3 29.8 1.0 CG B:ASP447 3.4 26.6 1.0 O3A B:TPP2702 3.4 31.1 1.0 ND2 B:ASN474 3.4 26.6 1.0 O2B B:TPP2702 3.8 29.6 1.0 OD2 B:ASP447 3.9 27.1 1.0 N B:GLN476 3.9 29.2 1.0 N B:ASP447 4.0 27.1 1.0 O7 B:TPP2702 4.0 32.8 1.0 N B:GLY478 4.1 31.1 1.0 N B:GLY448 4.1 28.0 1.0 CA B:GLN476 4.1 29.6 1.0 N B:TYR477 4.2 29.3 1.0 O B:PHE472 4.3 30.5 1.0 CA B:TYR477 4.4 30.0 1.0 O2A B:TPP2702 4.4 29.2 1.0 N B:ASN474 4.5 30.8 1.0 O1B B:TPP2702 4.5 31.2 1.0 CB B:ASP447 4.5 27.1 1.0 CB B:ASN474 4.6 30.9 1.0 CA B:ASP447 4.6 27.8 1.0 CB B:GLN476 4.6 30.3 1.0 CZ B:PHE497 4.6 31.1 1.0 C B:TYR477 4.8 30.6 1.0 C B:GLY446 4.8 26.5 1.0 C B:ASP447 4.8 28.0 1.0 CA B:GLY446 4.8 25.5 1.0 N B:CYS475 4.9 30.7 1.0 CA B:ASN474 4.9 31.1 1.0 CA B:GLY448 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2801 b:40.4 occ:1.00 OD1 C:ASN474 2.1 43.6 1.0 O C:GLN476 2.2 36.3 1.0 O1A C:TPP2802 2.2 37.1 1.0 O3B C:TPP2802 2.3 35.0 1.0 OD1 C:ASP447 2.3 37.1 1.0 CG C:ASN474 3.0 39.9 1.0 ND2 C:ASN474 3.2 36.2 1.0 PB C:TPP2802 3.3 37.4 1.0 PA C:TPP2802 3.3 33.4 1.0 C C:GLN476 3.4 36.2 1.0 O3A C:TPP2802 3.4 37.7 1.0 CG C:ASP447 3.4 34.7 1.0 O2B C:TPP2802 3.7 33.1 1.0 OD2 C:ASP447 3.9 38.6 1.0 O C:PHE472 4.0 36.4 1.0 N C:ASP447 4.0 33.8 1.0 N C:GLN476 4.0 37.8 1.0 O7 C:TPP2802 4.2 36.3 1.0 N C:GLY448 4.2 34.6 1.0 CA C:GLN476 4.2 37.5 1.0 N C:GLY478 4.3 35.7 1.0 N C:TYR477 4.4 36.0 1.0 N C:ASN474 4.4 38.4 1.0 O2A C:TPP2802 4.4 36.2 1.0 CB C:ASN474 4.4 38.6 1.0 CA C:TYR477 4.6 35.8 1.0 O1B C:TPP2802 4.6 37.6 1.0 CA C:GLY446 4.6 33.0 1.0 CB C:ASP447 4.7 34.1 1.0 N C:CYS475 4.7 38.4 1.0 CZ C:PHE497 4.7 40.1 1.0 CA C:ASP447 4.7 34.4 1.0 C C:GLY446 4.7 33.7 1.0 CB C:GLN476 4.8 37.1 1.0 CA C:ASN474 4.8 38.3 1.0 C C:ASN474 4.9 38.4 1.0 C C:TYR477 5.0 35.7 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Oxidase Variant V265A From Lactobacillus Plantarum within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2901 b:32.0 occ:1.00 O1A D:TPP2902 2.0 23.7 1.0 OD1 D:ASN474 2.1 39.2 1.0 O D:GLN476 2.1 28.3 1.0 O3B D:TPP2902 2.1 30.2 1.0 OD1 D:ASP447 2.2 30.4 1.0 O D:HOH2946 2.3 36.7 1.0 CG D:ASN474 3.0 35.7 1.0 ND2 D:ASN474 3.2 34.6 1.0 PA D:TPP2902 3.2 26.5 1.0 PB D:TPP2902 3.3 33.7 1.0 C D:GLN476 3.3 29.6 1.0 CG D:ASP447 3.3 29.3 1.0 O3A D:TPP2902 3.5 31.2 1.0 N D:GLN476 3.8 31.2 1.0 OD2 D:ASP447 3.8 30.0 1.0 O2B D:TPP2902 3.9 32.6 1.0 N D:GLY478 4.1 31.0 1.0 CA D:GLN476 4.1 30.7 1.0 O7 D:TPP2902 4.1 28.2 1.0 N D:ASP447 4.1 28.3 1.0 N D:GLY448 4.1 28.6 1.0 N D:TYR477 4.3 29.6 1.0 CA D:TYR477 4.4 30.0 1.0 O D:PHE472 4.4 31.6 1.0 CB D:ASN474 4.4 32.6 1.0 O2A D:TPP2902 4.4 28.8 1.0 O1B D:TPP2902 4.5 31.2 1.0 N D:ASN474 4.5 33.1 1.0 CZ D:PHE497 4.5 27.1 1.0 CB D:GLN476 4.6 32.0 1.0 CB D:ASP447 4.6 28.6 1.0 CA D:ASP447 4.7 27.8 1.0 N D:CYS475 4.7 32.8 1.0 C D:TYR477 4.8 30.1 1.0 CA D:ASN474 4.8 32.5 1.0 C D:GLY446 4.9 28.4 1.0 CA D:GLY446 4.9 27.7 1.0 C D:ASP447 4.9 28.9 1.0 C D:ASN474 4.9 33.3 1.0 C D:CYS475 5.0 31.4 1.0 CA D:GLY478 5.0 31.7 1.0 CA D:GLY448 5.0 29.0 1.0

G.Wille, M.Ritter, M.S.Weiss, S.Konig, W.Mantele, G.Hubner. The Role of Val-265 For Flavin Adenine Dinulceotide (Fad) Binding in Pyruvate Oxidase: Ftir, Kinetic and Crystallographic Studies on the Enzyme Variant V265A Biochemistry V. 44 5086 2005.
ISSN: ISSN 0006-2960
PubMed: 15794646
DOI: 10.1021/BI047337O