Magnesium in PDB 6vmf: Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine

The structure of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine, PDB code: 6vmf was solved by E.T.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.42 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.857, 92.985, 187.048, 90.00, 95.06, 90.00
R / Rfree (%)	20.2 / 25

The binding sites of Magnesium atom in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine (pdb code 6vmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine, PDB code: 6vmf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:38.9 occ:1.00 O A:ALA699 2.2 30.5 1.0 O A:ILE365 2.3 24.4 1.0 O A:ALA362 2.3 21.0 1.0 O A:HOH1033 2.5 36.7 1.0 OD1 A:ASN700 2.7 32.8 1.0 OD1 A:ASP360 2.9 36.8 1.0 C A:ALA699 3.1 21.5 1.0 C A:ALA362 3.3 17.9 1.0 C A:ILE365 3.4 21.5 1.0 OD2 A:ASP360 3.6 38.0 1.0 CG A:ASP360 3.6 31.2 1.0 CG A:ASN700 3.7 26.1 1.0 N A:ASN700 3.8 30.4 1.0 CA A:ASN700 3.8 21.6 1.0 CB A:ALA362 4.1 16.3 1.0 CA A:ALA362 4.1 19.6 1.0 N A:ILE365 4.1 22.1 1.0 N A:PRO363 4.2 17.1 1.0 CA A:ALA699 4.2 22.0 1.0 CB A:ALA699 4.2 34.2 1.0 CA A:ILE365 4.2 15.9 1.0 CA A:PRO363 4.2 25.3 1.0 CB A:ASN700 4.3 32.0 1.0 CB A:ILE365 4.3 17.2 1.0 C A:PRO363 4.4 27.4 1.0 N A:ALA362 4.4 33.0 1.0 N A:GLU366 4.5 27.0 1.0 O A:PRO363 4.5 34.2 1.0 CD A:PRO367 4.6 23.3 1.0 ND2 A:ASN700 4.7 31.0 1.0 CA A:GLU366 4.7 21.3 1.0 N A:GLN364 4.9 25.9 1.0 O A:ALA576 5.0 45.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:49.4 occ:1.00 O B:ALA699 2.3 38.4 1.0 OD1 B:ASN700 2.4 56.2 1.0 O B:ILE365 2.5 36.7 1.0 O B:ALA362 2.5 57.0 1.0 O B:HOH1006 2.6 38.6 1.0 OD1 B:ASP360 2.6 43.3 1.0 C B:ALA699 3.0 39.4 1.0 C B:ALA362 3.3 45.9 1.0 CG B:ASN700 3.5 53.5 1.0 CG B:ASP360 3.5 51.9 1.0 CA B:ASN700 3.5 51.9 1.0 N B:ASN700 3.6 45.6 1.0 OD2 B:ASP360 3.6 51.7 1.0 C B:ILE365 3.6 43.4 1.0 CA B:ALA699 4.0 37.1 1.0 CB B:ALA699 4.1 43.5 1.0 CA B:ALA362 4.1 42.0 1.0 CB B:ALA362 4.1 47.0 1.0 CB B:ASN700 4.1 54.4 1.0 N B:ALA362 4.2 37.2 1.0 N B:PRO363 4.2 38.5 1.0 N B:ILE365 4.3 41.3 1.0 CA B:PRO363 4.3 48.1 1.0 CA B:ILE365 4.3 35.9 1.0 CB B:ILE365 4.4 32.1 1.0 C B:PRO363 4.5 41.0 1.0 ND2 B:ASN700 4.5 49.5 1.0 O B:PRO363 4.7 44.8 1.0 N B:GLU366 4.7 50.1 1.0 C B:ASN700 4.8 44.9 1.0 CD B:PRO367 4.9 37.4 1.0 CA B:GLU366 4.9 52.1 1.0 CB B:ASP360 4.9 51.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:40.9 occ:1.00 O C:ILE365 2.1 25.6 1.0 O C:ALA699 2.3 34.0 1.0 O C:ALA362 2.3 34.1 1.0 O C:HOH1078 2.6 37.3 1.0 OD1 C:ASN700 2.8 39.8 1.0 OD1 C:ASP360 2.9 41.5 1.0 C C:ILE365 3.2 23.8 1.0 C C:ALA362 3.2 33.8 1.0 C C:ALA699 3.3 35.6 1.0 OD2 C:ASP360 3.6 54.0 1.0 CG C:ASP360 3.7 35.9 1.0 N C:ILE365 3.8 33.9 1.0 CA C:ILE365 3.8 22.5 1.0 CG C:ASN700 3.9 33.0 1.0 CB C:ILE365 3.9 26.1 1.0 CB C:ALA362 4.0 29.5 1.0 N C:ASN700 4.0 37.4 1.0 CA C:ASN700 4.0 35.9 1.0 CA C:ALA362 4.1 31.9 1.0 N C:PRO363 4.1 32.0 1.0 CA C:PRO363 4.1 36.3 1.0 C C:PRO363 4.2 38.3 1.0 CB C:ALA699 4.2 44.7 1.0 CA C:ALA699 4.3 36.0 1.0 N C:GLU366 4.3 27.4 1.0 N C:ALA362 4.4 44.9 1.0 O C:PRO363 4.4 31.0 1.0 CB C:ASN700 4.6 38.2 1.0 CA C:GLU366 4.6 24.9 1.0 N C:GLN364 4.7 30.8 1.0 CG2 C:ILE365 4.7 30.6 1.0 CD C:PRO367 4.7 27.0 1.0 ND2 C:ASN700 4.9 34.9 1.0 C C:GLN364 4.9 41.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:45.0 occ:1.00 O D:ILE365 2.2 26.3 1.0 O D:HOH1166 2.3 40.5 1.0 O D:ALA362 2.4 43.5 1.0 O D:ALA699 2.4 37.5 1.0 OD1 D:ASN700 2.5 43.3 1.0 OD1 D:ASP360 2.8 34.7 1.0 C D:ALA362 3.2 37.1 1.0 C D:ILE365 3.3 33.1 1.0 C D:ALA699 3.4 31.2 1.0 OD2 D:ASP360 3.4 42.0 1.0 CG D:ASP360 3.5 36.5 1.0 CG D:ASN700 3.6 31.8 1.0 N D:ILE365 3.9 38.0 1.0 CA D:ASN700 3.9 35.8 1.0 CA D:ILE365 4.0 30.8 1.0 N D:PRO363 4.0 33.2 1.0 CA D:PRO363 4.0 37.1 1.0 N D:ASN700 4.0 34.3 1.0 CA D:ALA362 4.0 43.3 1.0 CB D:ALA362 4.1 30.1 1.0 CB D:ILE365 4.1 33.2 1.0 C D:PRO363 4.2 40.7 1.0 N D:ALA362 4.2 54.5 1.0 CB D:ALA699 4.4 38.5 1.0 O D:PRO363 4.4 40.5 1.0 CA D:ALA699 4.4 27.7 1.0 CB D:ASN700 4.4 37.6 1.0 N D:GLU366 4.4 35.0 1.0 ND2 D:ASN700 4.6 37.1 1.0 CA D:GLU366 4.7 28.5 1.0 N D:GLN364 4.8 34.4 1.0 CD D:PRO367 4.8 35.1 1.0 CG2 D:ILE365 4.8 25.6 1.0 CB D:ASP360 5.0 38.9 1.0

K.J.Mamounis, E.T.Yukl, V.L.Davidson. Roles of Active Site Residues in Catalysis, Substrate Binding, Cooperativity and the Reaction Mechanism of the Quinoprotein Glycine Oxidase J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X