Magnesium in PDB 6ubr: Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5

The structure of Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5, PDB code: 6ubr was solved by E.T.Yukl, D.Avalos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	110.679, 93.348, 187.853, 90.00, 94.95, 90.00
R / Rfree (%)	17.5 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5 (pdb code 6ubr). 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 D678A Goxa Bound to Glycine at pH 7.5, PDB code: 6ubr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5


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 D678A Goxa Bound to Glycine at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:21.5 occ:1.00 O B:ALA699 2.3 16.9 1.0 O B:ALA362 2.3 16.7 1.0 O B:ILE365 2.4 15.9 1.0 OD1 B:ASN700 2.4 21.0 1.0 O B:HOH1216 2.6 27.2 1.0 OD1 B:ASP360 2.8 15.4 1.0 HA B:ASN700 3.0 26.1 1.0 C B:ALA699 3.2 15.1 1.0 C B:ALA362 3.3 22.6 1.0 HB3 B:ALA362 3.4 19.7 1.0 OD2 B:ASP360 3.5 23.7 1.0 CG B:ASN700 3.5 18.1 1.0 CG B:ASP360 3.5 36.6 1.0 C B:ILE365 3.5 17.9 1.0 HB1 B:ALA699 3.5 22.1 1.0 H B:ILE365 3.6 25.8 1.0 HB B:ILE365 3.6 21.7 1.0 HA B:PRO363 3.6 21.5 1.0 H B:ALA362 3.7 20.9 1.0 CA B:ASN700 3.7 21.8 1.0 N B:ASN700 3.8 18.6 1.0 HD3 B:PRO367 3.8 18.9 1.0 CA B:ALA362 4.1 17.5 1.0 N B:PRO363 4.1 20.0 1.0 CB B:ALA362 4.1 16.5 1.0 N B:ILE365 4.2 21.5 1.0 CA B:PRO363 4.2 17.9 1.0 O B:HOH1332 4.2 31.7 1.0 HA B:GLU366 4.2 19.6 1.0 CA B:ALA699 4.2 16.8 1.0 CB B:ASN700 4.2 17.8 1.0 CB B:ALA699 4.2 18.5 1.0 CA B:ILE365 4.2 20.6 1.0 N B:ALA362 4.3 17.4 1.0 CB B:ILE365 4.3 18.1 1.0 C B:PRO363 4.4 21.9 1.0 HA B:ALA699 4.4 20.1 1.0 HB3 B:ALA699 4.4 22.1 1.0 HB1 B:ALA362 4.4 19.7 1.0 ND2 B:ASN700 4.5 22.2 1.0 HD21 B:ASN700 4.5 26.6 1.0 O B:PRO363 4.5 17.9 1.0 H B:ASN700 4.6 22.2 1.0 N B:GLU366 4.6 17.0 1.0 HB3 B:ASN700 4.7 21.4 1.0 HG22 B:ILE365 4.7 22.5 1.0 CD B:PRO367 4.8 15.8 1.0 CA B:GLU366 4.8 16.4 1.0 HG3 B:PRO367 4.8 25.3 1.0 HB2 B:ASN700 4.9 21.4 1.0 HB2 B:ALA362 4.9 19.7 1.0 N B:GLN364 5.0 20.9 1.0 O B:ALA576 5.0 28.1 1.0 CB B:ASP360 5.0 18.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5


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 D678A Goxa Bound to Glycine at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:26.6 occ:1.00 O A:ALA362 2.3 20.5 1.0 O A:ALA699 2.3 20.4 1.0 O A:ILE365 2.4 25.6 1.0 O A:HOH1031 2.5 26.8 1.0 OD1 A:ASN700 2.6 25.3 1.0 OD1 A:ASP360 2.6 26.1 1.0 HA A:ASN700 3.0 28.7 1.0 C A:ALA699 3.2 18.3 1.0 C A:ALA362 3.2 32.3 1.0 OD2 A:ASP360 3.3 31.8 1.0 CG A:ASP360 3.3 30.2 1.0 HB3 A:ALA362 3.4 25.4 1.0 HB A:ILE365 3.5 28.4 1.0 H A:ILE365 3.5 23.5 1.0 C A:ILE365 3.6 26.4 1.0 CG A:ASN700 3.6 32.5 1.0 HA A:PRO363 3.6 32.4 1.0 HB1 A:ALA699 3.6 25.8 1.0 H A:ALA362 3.7 31.8 1.0 CA A:ASN700 3.8 24.0 1.0 N A:ASN700 3.8 19.0 1.0 HD3 A:PRO367 4.0 20.7 1.0 N A:PRO363 4.1 22.0 1.0 CA A:ALA362 4.1 29.3 1.0 CA A:PRO363 4.1 27.1 1.0 N A:ILE365 4.1 19.7 1.0 CB A:ALA362 4.1 21.2 1.0 CA A:ILE365 4.2 22.0 1.0 O A:HOH1233 4.2 28.0 1.0 N A:ALA362 4.3 26.5 1.0 CB A:ILE365 4.3 23.7 1.0 CB A:ASN700 4.3 23.6 1.0 HA A:GLU366 4.3 25.9 1.0 CA A:ALA699 4.3 22.5 1.0 CB A:ALA699 4.3 21.6 1.0 C A:PRO363 4.3 29.1 1.0 HB1 A:ALA362 4.4 25.4 1.0 HA A:ALA699 4.4 26.9 1.0 HB3 A:ALA699 4.5 25.8 1.0 ND2 A:ASN700 4.5 28.7 1.0 HD21 A:ASN700 4.6 34.4 1.0 O A:PRO363 4.6 27.5 1.0 H A:ASN700 4.6 22.7 1.0 N A:GLU366 4.7 23.3 1.0 HG22 A:ILE365 4.7 36.1 1.0 HB3 A:ASN700 4.7 28.3 1.0 HG3 A:PRO367 4.8 32.3 1.0 CB A:ASP360 4.8 18.5 1.0 CD A:PRO367 4.9 17.3 1.0 CA A:GLU366 4.9 21.6 1.0 N A:GLN364 4.9 22.7 1.0 HB2 A:ALA362 5.0 25.4 1.0 HA A:ALA362 5.0 35.1 1.0 O A:ALA576 5.0 33.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5


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 D678A Goxa Bound to Glycine at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:23.0 occ:1.00 O C:ALA362 2.3 17.9 1.0 O C:ILE365 2.4 21.1 1.0 OD1 C:ASN700 2.4 24.2 1.0 O C:ALA699 2.4 22.5 1.0 O C:HOH1176 2.5 23.6 1.0 OD1 C:ASP360 2.7 21.1 1.0 HA C:ASN700 3.0 23.5 1.0 C C:ALA362 3.2 24.8 1.0 OD2 C:ASP360 3.2 27.5 1.0 C C:ALA699 3.3 18.6 1.0 CG C:ASP360 3.3 27.3 1.0 HB3 C:ALA362 3.4 16.9 1.0 CG C:ASN700 3.5 21.8 1.0 C C:ILE365 3.5 19.9 1.0 HA C:PRO363 3.5 24.5 1.0 H C:ILE365 3.6 29.2 1.0 HB C:ILE365 3.6 24.0 1.0 H C:ALA362 3.6 25.1 1.0 HB1 C:ALA699 3.7 27.1 1.0 CA C:ASN700 3.8 19.6 1.0 N C:ASN700 3.9 18.0 1.0 HD3 C:PRO367 3.9 25.6 1.0 N C:PRO363 4.0 23.3 1.0 CA C:PRO363 4.0 20.4 1.0 CA C:ALA362 4.1 19.4 1.0 CB C:ALA362 4.1 14.1 1.0 N C:ILE365 4.1 24.4 1.0 HA C:GLU366 4.2 21.7 1.0 O C:HOH1349 4.2 30.2 1.0 CB C:ASN700 4.2 20.1 1.0 CA C:ILE365 4.2 20.0 1.0 N C:ALA362 4.2 20.9 1.0 C C:PRO363 4.3 22.1 1.0 CA C:ALA699 4.3 14.8 1.0 CB C:ILE365 4.3 20.0 1.0 CB C:ALA699 4.4 22.6 1.0 HB1 C:ALA362 4.4 16.9 1.0 O C:PRO363 4.4 17.5 1.0 ND2 C:ASN700 4.4 27.4 1.0 HD21 C:ASN700 4.4 32.8 1.0 HB3 C:ALA699 4.5 27.1 1.0 HA C:ALA699 4.5 17.7 1.0 N C:GLU366 4.6 22.9 1.0 H C:ASN700 4.7 21.6 1.0 HB3 C:ASN700 4.7 24.1 1.0 HG22 C:ILE365 4.7 25.8 1.0 HG3 C:PRO367 4.8 30.2 1.0 CB C:ASP360 4.8 17.7 1.0 CA C:GLU366 4.8 18.1 1.0 CD C:PRO367 4.8 21.4 1.0 N C:GLN364 4.9 19.8 1.0 O C:ALA576 4.9 29.1 1.0 HA C:ALA362 4.9 23.2 1.0 HB2 C:ALA362 5.0 16.9 1.0 HB2 C:ASN700 5.0 24.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 7.5


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 D678A Goxa Bound to Glycine at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:28.2 occ:1.00 O D:ALA699 2.3 23.3 1.0 O D:ALA362 2.4 27.1 1.0 O D:ILE365 2.4 27.0 1.0 OD1 D:ASN700 2.4 27.2 1.0 O D:HOH1033 2.5 27.0 1.0 OD1 D:ASP360 2.7 28.4 1.0 HA D:ASN700 3.0 37.0 1.0 OD2 D:ASP360 3.2 36.8 1.0 C D:ALA699 3.2 20.6 1.0 C D:ALA362 3.3 31.9 1.0 CG D:ASP360 3.3 27.4 1.0 HB3 D:ALA362 3.4 31.0 1.0 CG D:ASN700 3.5 27.5 1.0 C D:ILE365 3.6 24.5 1.0 HB D:ILE365 3.6 30.9 1.0 H D:ILE365 3.6 27.0 1.0 HA D:PRO363 3.6 31.2 1.0 HB1 D:ALA699 3.6 34.6 1.0 H D:ALA362 3.7 31.0 1.0 CA D:ASN700 3.7 30.9 1.0 N D:ASN700 3.8 26.1 1.0 HD3 D:PRO367 4.0 35.0 1.0 CA D:ALA362 4.1 31.1 1.0 N D:PRO363 4.1 23.5 1.0 CB D:ALA362 4.1 25.8 1.0 CA D:PRO363 4.1 26.1 1.0 N D:ILE365 4.2 22.5 1.0 CB D:ASN700 4.2 21.3 1.0 HA D:GLU366 4.2 24.7 1.0 CA D:ILE365 4.2 25.8 1.0 CA D:ALA699 4.3 15.1 1.0 N D:ALA362 4.3 25.9 1.0 CB D:ALA699 4.3 28.9 1.0 O D:HOH1334 4.3 41.9 1.0 CB D:ILE365 4.3 25.8 1.0 C D:PRO363 4.4 34.4 1.0 HB1 D:ALA362 4.4 31.0 1.0 HA D:ALA699 4.4 18.1 1.0 ND2 D:ASN700 4.5 30.1 1.0 HB3 D:ALA699 4.5 34.6 1.0 HD21 D:ASN700 4.5 36.0 1.0 O D:PRO363 4.6 33.6 1.0 HB3 D:ASN700 4.6 25.5 1.0 H D:ASN700 4.6 31.3 1.0 N D:GLU366 4.6 25.0 1.0 HG3 D:PRO367 4.8 38.4 1.0 HG22 D:ILE365 4.8 33.3 1.0 CB D:ASP360 4.8 28.8 1.0 CA D:GLU366 4.8 20.6 1.0 CD D:PRO367 4.9 29.2 1.0 N D:GLN364 4.9 25.0 1.0 HB2 D:ALA362 4.9 31.0 1.0 HB2 D:ASN700 5.0 25.5 1.0 HA D:ALA362 5.0 37.3 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