Magnesium in PDB 6ubn: Crystal Structure of D678E Goxa Bound to Glycine

The structure of Crystal Structure of D678E Goxa Bound to Glycine, PDB code: 6ubn 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)	47.31 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	110.239, 92.132, 178.443, 90.00, 91.16, 90.00
R / Rfree (%)	17 / 22.2

The structure of Crystal Structure of D678E Goxa Bound to Glycine also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of D678E Goxa Bound to Glycine (pdb code 6ubn). 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 D678E Goxa Bound to Glycine, PDB code: 6ubn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D678E Goxa Bound to 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 D678E Goxa Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:28.3 occ:1.00 O A:ILE365 2.3 19.6 1.0 O A:ALA362 2.3 21.0 1.0 O A:ALA699 2.3 28.4 1.0 O A:HOH1051 2.4 31.8 1.0 OD1 A:ASN700 2.5 23.5 1.0 OD1 A:ASP360 2.9 18.1 1.0 C A:ALA699 3.2 23.4 1.0 C A:ALA362 3.2 22.6 1.0 C A:ILE365 3.4 25.2 1.0 OD2 A:ASP360 3.5 27.7 1.0 CG A:ASP360 3.6 25.8 1.0 CG A:ASN700 3.6 24.0 1.0 CA A:ASN700 3.8 23.5 1.0 N A:ASN700 3.8 23.7 1.0 CB A:ALA362 3.9 19.8 1.0 CA A:ALA362 4.0 20.9 1.0 N A:ILE365 4.0 20.4 1.0 N A:PRO363 4.0 22.6 1.0 CA A:ILE365 4.1 21.0 1.0 CA A:PRO363 4.2 16.2 1.0 CB A:ILE365 4.2 20.7 1.0 CA A:ALA699 4.2 10.5 1.0 CB A:ALA699 4.2 11.8 1.0 N A:ALA362 4.2 25.8 1.0 CB A:ASN700 4.3 26.3 1.0 C A:PRO363 4.3 26.2 1.0 O A:HOH1244 4.4 42.7 1.0 O A:PRO363 4.5 21.6 1.0 N A:GLU366 4.5 20.2 1.0 ND2 A:ASN700 4.6 24.0 1.0 CD A:PRO367 4.7 14.3 1.0 CA A:GLU366 4.8 16.3 1.0 N A:GLN364 4.9 24.0 1.0 CG2 A:ILE365 5.0 19.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D678E Goxa Bound to 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 D678E Goxa Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:25.6 occ:1.00 O B:ALA699 2.3 22.2 1.0 O B:ALA362 2.3 19.0 1.0 O B:HOH1072 2.4 34.3 1.0 O B:ILE365 2.4 23.7 1.0 OD1 B:ASN700 2.6 25.6 1.0 OD1 B:ASP360 2.6 23.9 1.0 C B:ALA362 3.1 26.7 1.0 C B:ALA699 3.2 20.9 1.0 OD2 B:ASP360 3.2 32.1 1.0 CG B:ASP360 3.3 26.8 1.0 CG B:ASN700 3.5 25.9 1.0 C B:ILE365 3.6 24.7 1.0 CA B:ASN700 3.7 27.5 1.0 N B:ASN700 3.8 22.2 1.0 CA B:ALA362 3.9 30.9 1.0 CB B:ALA362 3.9 23.6 1.0 N B:PRO363 4.0 24.6 1.0 CA B:PRO363 4.1 28.0 1.0 N B:ALA362 4.1 27.8 1.0 N B:ILE365 4.2 25.8 1.0 CB B:ASN700 4.2 17.2 1.0 CA B:ILE365 4.3 20.1 1.0 CA B:ALA699 4.3 17.1 1.0 CB B:ALA699 4.3 18.9 1.0 C B:PRO363 4.3 25.2 1.0 CB B:ILE365 4.4 20.5 1.0 O B:HOH1231 4.4 37.2 1.0 ND2 B:ASN700 4.5 34.6 1.0 O B:PRO363 4.5 24.5 1.0 N B:GLU366 4.7 24.8 1.0 CB B:ASP360 4.8 22.3 1.0 CA B:GLU366 4.9 29.6 1.0 CD B:PRO367 4.9 17.9 1.0 N B:GLN364 4.9 25.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D678E Goxa Bound to 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 D678E Goxa Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:27.7 occ:1.00 O C:ALA362 2.3 17.4 1.0 O C:ILE365 2.3 22.6 1.0 O C:HOH1003 2.3 36.3 1.0 O C:ALA699 2.3 27.6 1.0 OD1 C:ASN700 2.5 26.5 1.0 OD1 C:ASP360 2.9 21.0 1.0 C C:ALA362 3.2 24.5 1.0 C C:ALA699 3.3 27.5 1.0 OD2 C:ASP360 3.3 30.3 1.0 C C:ILE365 3.4 26.3 1.0 CG C:ASP360 3.5 27.9 1.0 CG C:ASN700 3.6 25.2 1.0 CA C:ASN700 3.9 23.6 1.0 N C:ASN700 3.9 27.7 1.0 N C:PRO363 4.0 26.8 1.0 CA C:ALA362 4.0 17.9 1.0 N C:ILE365 4.0 20.7 1.0 CA C:PRO363 4.1 18.8 1.0 CB C:ALA362 4.1 12.7 1.0 CA C:ILE365 4.1 25.3 1.0 O C:HOH1335 4.2 38.4 1.0 CB C:ILE365 4.3 29.0 1.0 N C:ALA362 4.3 24.1 1.0 CA C:ALA699 4.3 13.5 1.0 C C:PRO363 4.3 33.1 1.0 CB C:ASN700 4.3 17.4 1.0 CB C:ALA699 4.3 25.4 1.0 N C:GLU366 4.4 23.0 1.0 O C:PRO363 4.6 29.4 1.0 ND2 C:ASN700 4.7 27.7 1.0 CA C:GLU366 4.7 11.7 1.0 CD C:PRO367 4.8 25.1 1.0 N C:GLN364 4.9 28.5 1.0 CG2 C:ILE365 5.0 30.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D678E Goxa Bound to 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 D678E Goxa Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:39.8 occ:1.00 O D:ALA362 2.3 32.5 1.0 O D:ILE365 2.4 29.4 1.0 O D:ALA699 2.4 30.4 1.0 O D:HOH1066 2.6 36.9 1.0 OD1 D:ASP360 2.6 27.4 1.0 OD1 D:ASN700 2.6 40.1 1.0 C D:ALA362 3.2 32.1 1.0 C D:ALA699 3.3 32.4 1.0 OD2 D:ASP360 3.3 34.7 1.0 CG D:ASP360 3.3 31.7 1.0 C D:ILE365 3.5 32.4 1.0 CG D:ASN700 3.6 40.1 1.0 CA D:ASN700 3.7 26.0 1.0 N D:ASN700 3.8 25.8 1.0 CA D:ALA362 4.0 30.1 1.0 N D:PRO363 4.0 31.4 1.0 CB D:ALA362 4.0 31.8 1.0 CA D:PRO363 4.1 33.9 1.0 N D:ALA362 4.1 24.9 1.0 N D:ILE365 4.2 28.6 1.0 CA D:ILE365 4.2 28.4 1.0 CB D:ASN700 4.2 26.3 1.0 CA D:ALA699 4.3 32.6 1.0 C D:PRO363 4.3 31.8 1.0 CB D:ILE365 4.4 30.1 1.0 CB D:ALA699 4.4 23.5 1.0 O D:PRO363 4.5 31.9 1.0 O D:HOH1302 4.5 39.1 1.0 N D:GLU366 4.6 35.6 1.0 ND2 D:ASN700 4.6 32.9 1.0 CB D:ASP360 4.8 24.3 1.0 CA D:GLU366 4.9 34.4 1.0 N D:GLN364 4.9 30.4 1.0 C D:ASN700 5.0 30.2 1.0 CD D:PRO367 5.0 26.2 1.0

K.J.Mamounis, D.Avalos, E.T.Yukl, V.L.Davidson. Kinetic and Structural Evidence That Asp-678 Plays Multiple Roles in Catalysis By the Quinoprotein Glycine Oxidase. J.Biol.Chem. V. 294 17463 2019.
ISSN: ESSN 1083-351X
PubMed: 31615898
DOI: 10.1074/JBC.RA119.011255