Sodium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6eer:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium 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 Sodium with other atoms in the Na 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:Na902 b:38.3 occ:1.00 O A:HOH1331 2.3 36.8 1.0 OG A:SER438 2.4 30.6 1.0 OG A:SER440 2.4 33.2 1.0 O A:HOH1610 2.4 48.5 1.0 O A:HOH1472 2.5 31.9 1.0 O A:HOH1621 2.5 47.5 1.0 CB A:SER438 3.3 27.8 1.0 CB A:SER440 3.3 32.5 1.0 N A:SER440 4.0 29.4 1.0 O A:HOH1024 4.2 45.1 1.0 O A:HOH1685 4.2 58.9 1.0 OD2 A:ASP436 4.3 31.8 1.0 CA A:SER440 4.3 30.7 1.0 O A:HOH1696 4.3 45.3 1.0 OD1 A:ASP436 4.6 29.6 1.0 CA A:SER438 4.6 26.8 1.0 C A:SER438 4.7 26.3 1.0 N A:ALA439 4.7 28.0 1.0 CG A:ASP436 4.8 29.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na902 b:45.0 occ:1.00 O B:HOH1582 2.3 38.9 1.0 O B:HOH1573 2.4 42.8 1.0 O B:HOH1175 2.4 42.4 1.0 OG B:SER438 2.4 28.9 1.0 O B:HOH1545 2.4 38.5 1.0 OG B:SER440 2.6 35.1 1.0 CB B:SER438 3.2 23.9 1.0 CB B:SER440 3.5 27.7 1.0 N B:SER440 4.1 22.8 1.0 O B:HOH1528 4.3 61.8 1.0 CA B:SER440 4.4 23.5 1.0 OD2 B:ASP436 4.5 34.0 1.0 O B:HOH1048 4.5 44.4 1.0 CA B:SER438 4.6 29.9 1.0 OD1 B:ASP436 4.6 32.1 1.0 C B:SER438 4.7 26.6 1.0 N B:ALA439 4.8 28.8 1.0 CG B:ASP436 5.0 34.6 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na902 b:41.7 occ:1.00 O C:HOH1130 2.3 38.0 1.0 OG C:SER438 2.3 32.4 1.0 O C:HOH1510 2.4 30.7 1.0 OG C:SER440 2.5 31.6 1.0 O C:HOH1635 2.7 41.4 1.0 CB C:SER438 3.3 26.2 1.0 CB C:SER440 3.4 28.6 1.0 N C:SER440 4.0 29.8 1.0 OD2 C:ASP436 4.1 34.8 1.0 O C:HOH1705 4.3 64.1 1.0 CA C:SER440 4.3 32.1 1.0 OD1 C:ASP436 4.5 27.8 1.0 CA C:SER438 4.5 26.4 1.0 C C:SER438 4.7 23.2 1.0 O C:HOH1653 4.7 49.3 1.0 N C:ALA439 4.7 24.9 1.0 CG C:ASP436 4.7 35.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na902 b:37.9 occ:1.00 O D:HOH1556 2.3 43.4 1.0 O D:HOH1565 2.3 41.9 1.0 O D:HOH1044 2.3 39.1 1.0 O D:HOH1517 2.4 28.4 1.0 OG D:SER438 2.4 32.3 1.0 OG D:SER440 2.5 31.4 1.0 CB D:SER438 3.3 30.9 1.0 CB D:SER440 3.4 23.8 1.0 O D:HOH1554 3.9 46.1 1.0 N D:SER440 4.1 23.3 1.0 OD2 D:ASP436 4.2 39.6 1.0 CA D:SER440 4.3 22.5 1.0 O D:HOH1150 4.4 35.8 1.0 OD1 D:ASP436 4.5 36.8 1.0 CA D:SER438 4.6 27.3 1.0 C D:SER438 4.7 22.6 1.0 CG D:ASP436 4.7 36.2 1.0 N D:ALA439 4.8 26.4 1.0 O D:HOH1313 5.0 51.7 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