Magnesium in PDB 6eer: Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea

The structure of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6eer 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)	48.30 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	110.242, 93.464, 187.903, 90.00, 95.02, 90.00
R / Rfree (%)	17.6 / 21.3

The structure of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea (pdb code 6eer). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6eer:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:15.5 occ:1.00 O A:ILE365 2.2 14.3 1.0 O A:ALA699 2.3 16.0 1.0 O A:ALA362 2.3 11.9 1.0 OD1 A:ASN700 2.4 17.0 1.0 O A:HOH1131 2.5 22.3 1.0 OD1 A:ASP360 2.8 17.4 1.0 C A:ALA699 3.2 15.8 1.0 C A:ALA362 3.2 15.5 1.0 C A:ILE365 3.4 13.6 1.0 OD2 A:ASP360 3.5 21.7 1.0 CG A:ASN700 3.5 19.4 1.0 CG A:ASP360 3.5 19.4 1.0 CA A:ASN700 3.8 17.0 1.0 N A:ASN700 3.9 13.2 1.0 CA A:ALA362 4.1 11.8 1.0 N A:PRO363 4.1 11.9 1.0 N A:ILE365 4.1 14.0 1.0 CB A:ALA362 4.1 13.9 1.0 CA A:ILE365 4.1 14.6 1.0 CA A:PRO363 4.1 16.0 1.0 O A:HOH1515 4.2 26.8 1.0 CB A:ALA699 4.2 12.3 1.0 CA A:ALA699 4.2 11.6 1.0 CB A:ILE365 4.2 14.1 1.0 CB A:ASN700 4.2 13.3 1.0 N A:ALA362 4.3 13.2 1.0 C A:PRO363 4.3 16.5 1.0 N A:GLU366 4.4 13.2 1.0 ND2 A:ASN700 4.5 19.1 1.0 O A:PRO363 4.5 13.1 1.0 CD A:PRO367 4.7 12.0 1.0 CA A:GLU366 4.8 13.2 1.0 N A:GLN364 4.9 11.9 1.0 CB A:ASP360 4.9 17.4 1.0 O A:ALA576 5.0 23.6 1.0

Magnesium binding site 2 out of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:24.9 occ:1.00 O B:ILE365 2.3 19.2 1.0 O B:ALA362 2.4 18.0 1.0 O B:HOH1039 2.4 18.7 1.0 O B:ALA699 2.5 20.0 1.0 OD1 B:ASN700 2.5 21.0 1.0 OD1 B:ASP360 2.7 20.1 1.0 OD2 B:ASP360 3.3 25.5 1.0 C B:ALA362 3.3 20.2 1.0 C B:ALA699 3.3 18.5 1.0 CG B:ASP360 3.4 20.6 1.0 C B:ILE365 3.4 19.3 1.0 CG B:ASN700 3.5 25.9 1.0 CA B:ASN700 3.8 17.3 1.0 N B:ASN700 3.9 20.6 1.0 N B:PRO363 4.1 19.6 1.0 CA B:ALA362 4.1 18.6 1.0 N B:ILE365 4.1 16.9 1.0 CA B:PRO363 4.1 17.8 1.0 CB B:ALA362 4.1 16.6 1.0 CA B:ILE365 4.1 16.5 1.0 O B:HOH1361 4.1 29.6 1.0 CB B:ALA699 4.2 15.2 1.0 CB B:ILE365 4.3 15.9 1.0 CA B:ALA699 4.3 16.7 1.0 N B:ALA362 4.3 17.4 1.0 CB B:ASN700 4.3 18.1 1.0 C B:PRO363 4.3 20.9 1.0 ND2 B:ASN700 4.5 24.9 1.0 N B:GLU366 4.5 20.9 1.0 O B:PRO363 4.5 27.1 1.0 CA B:GLU366 4.8 19.9 1.0 CD B:PRO367 4.9 20.2 1.0 N B:GLN364 4.9 17.8 1.0 CB B:ASP360 4.9 20.3 1.0

Magnesium binding site 3 out of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:18.5 occ:1.00 O C:ALA699 2.3 15.2 1.0 O C:ILE365 2.3 11.8 1.0 O C:ALA362 2.3 12.6 1.0 OD1 C:ASN700 2.4 16.9 1.0 O C:HOH1103 2.5 19.6 1.0 OD1 C:ASP360 2.8 16.6 1.0 C C:ALA699 3.2 17.4 1.0 C C:ALA362 3.3 16.9 1.0 OD2 C:ASP360 3.4 21.1 1.0 C C:ILE365 3.4 11.8 1.0 CG C:ASP360 3.5 19.1 1.0 CG C:ASN700 3.5 18.5 1.0 CA C:ASN700 3.8 16.3 1.0 N C:ASN700 3.9 11.9 1.0 CB C:ALA699 4.1 13.0 1.0 CA C:ALA362 4.1 13.8 1.0 N C:ILE365 4.1 14.7 1.0 N C:PRO363 4.1 13.8 1.0 CA C:PRO363 4.1 15.8 1.0 CB C:ALA362 4.1 13.4 1.0 CA C:ILE365 4.2 15.9 1.0 CA C:ALA699 4.2 14.0 1.0 O C:HOH1380 4.2 26.0 1.0 CB C:ASN700 4.2 13.9 1.0 N C:ALA362 4.3 13.6 1.0 C C:PRO363 4.3 17.0 1.0 CB C:ILE365 4.3 11.6 1.0 ND2 C:ASN700 4.4 17.1 1.0 N C:GLU366 4.5 12.0 1.0 O C:PRO363 4.5 14.0 1.0 CA C:GLU366 4.7 12.5 1.0 CD C:PRO367 4.8 11.8 1.0 N C:GLN364 4.9 16.1 1.0 CB C:ASP360 4.9 16.5 1.0 O C:ALA576 5.0 21.9 1.0

Magnesium binding site 4 out of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:23.6 occ:1.00 O D:ALA699 2.2 19.6 1.0 O D:ILE365 2.3 19.6 1.0 O D:ALA362 2.3 20.2 1.0 OD1 D:ASN700 2.4 17.7 1.0 O D:HOH1262 2.5 23.7 1.0 OD1 D:ASP360 2.8 20.9 1.0 C D:ALA699 3.1 17.8 1.0 C D:ALA362 3.2 24.4 1.0 C D:ILE365 3.5 16.5 1.0 CG D:ASN700 3.5 21.4 1.0 CG D:ASP360 3.6 24.0 1.0 OD2 D:ASP360 3.6 24.9 1.0 CA D:ASN700 3.8 23.9 1.0 N D:ASN700 3.8 18.4 1.0 CA D:ALA362 4.0 16.0 1.0 N D:PRO363 4.0 21.3 1.0 CB D:ALA362 4.1 17.4 1.0 CA D:PRO363 4.1 26.7 1.0 CB D:ALA699 4.1 15.1 1.0 CA D:ALA699 4.1 14.8 1.0 N D:ILE365 4.1 16.8 1.0 CA D:ILE365 4.2 16.4 1.0 N D:ALA362 4.2 17.6 1.0 CB D:ILE365 4.2 15.9 1.0 CB D:ASN700 4.2 20.6 1.0 O D:HOH1320 4.3 32.8 1.0 C D:PRO363 4.4 26.7 1.0 ND2 D:ASN700 4.5 22.4 1.0 N D:GLU366 4.5 16.7 1.0 O D:PRO363 4.6 29.9 1.0 CA D:GLU366 4.8 16.8 1.0 CD D:PRO367 4.8 18.1 1.0 N D:GLN364 4.9 17.6 1.0 CG2 D:ILE365 5.0 17.9 1.0

D.Avalos, S.Sabuncu, K.J.Mamounis, V.L.Davidson, P.Moenne-Loccoz, E.T.Yukl. Structural and Spectroscopic Characterization of A Product Schiff Base Intermediate in the Reaction of the Quinoprotein Glycine Oxidase, Goxa. Biochemistry V. 58 706 2019.
ISSN: ISSN 1520-4995
PubMed: 30605596
DOI: 10.1021/ACS.BIOCHEM.8B01145