Sodium in PDB 8jzh: C. Glutamicum S-Adenosylmethionine Synthase

All present enzymatic activity of C. Glutamicum S-Adenosylmethionine Synthase:
2.5.1.6;

The structure of C. Glutamicum S-Adenosylmethionine Synthase, PDB code: 8jzh was solved by S.Lee, K.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 2.20
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.152, 203.886, 144.186, 90, 90, 90
R / Rfree (%)	18.3 / 22.9

The binding sites of Sodium atom in the C. Glutamicum S-Adenosylmethionine Synthase (pdb code 8jzh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the C. Glutamicum S-Adenosylmethionine Synthase, PDB code: 8jzh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the C. Glutamicum S-Adenosylmethionine Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C. Glutamicum S-Adenosylmethionine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:25.3 occ:1.00 OD2 A:ASP191 2.2 38.7 1.0 OD1 A:ASP191 2.5 41.6 1.0 CG A:ASP191 2.7 47.0 1.0 CB A:ASP191 4.2 38.7 1.0 NH2 A:ARG8 4.5 39.1 1.0 NH1 A:ARG8 4.5 33.7 1.0 O A:ALA189 4.5 38.0 1.0 O A:HOH768 4.8 47.0 1.0 CZ A:ARG8 4.9 37.1 1.0 O A:HOH853 5.0 46.1 1.0

Sodium binding site 2 out of 3 in the C. Glutamicum S-Adenosylmethionine Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C. Glutamicum S-Adenosylmethionine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:29.5 occ:1.00 OD1 C:ASP191 2.3 38.1 1.0 OE2 B:GLU333 2.4 47.1 1.0 OE1 B:GLU333 2.5 47.8 1.0 OD2 C:ASP191 2.6 39.6 1.0 CG C:ASP191 2.8 42.1 1.0 CD B:GLU333 2.8 46.8 1.0 NH1 C:ARG8 4.1 46.3 1.0 CB C:ASP191 4.3 42.5 1.0 CG B:GLU333 4.3 43.9 1.0 NH2 C:ARG8 4.3 45.5 1.0 OD2 B:ASP344 4.4 46.5 1.0 O C:HOH604 4.4 43.1 1.0 O C:ALA189 4.6 49.3 1.0 CZ C:ARG8 4.6 41.9 1.0 O B:HOH601 4.9 40.3 1.0 O B:HOH605 4.9 34.5 1.0 N B:PHE335 4.9 43.9 1.0

Sodium binding site 3 out of 3 in the C. Glutamicum S-Adenosylmethionine Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of C. Glutamicum S-Adenosylmethionine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:32.9 occ:1.00 OD2 B:ASP191 2.2 46.4 1.0 OE2 C:GLU333 2.5 44.8 1.0 OE1 C:GLU333 2.6 52.1 1.0 OD1 B:ASP191 2.7 39.7 1.0 CG B:ASP191 2.8 41.0 1.0 CD C:GLU333 2.9 46.4 1.0 NH1 B:ARG8 4.1 49.7 1.0 CB B:ASP191 4.2 42.2 1.0 OD2 C:ASP344 4.3 50.3 1.0 CG C:GLU333 4.4 40.9 1.0 NH2 B:ARG8 4.6 46.1 1.0 O B:ALA189 4.6 49.1 1.0 O C:HOH649 4.7 43.6 1.0 CZ B:ARG8 4.8 46.5 1.0 OD1 C:ASP336 4.8 48.6 1.0 O B:HOH648 4.9 45.4 1.0 N C:PHE335 5.0 40.0 1.0

S.Lee, S.Kim, I.K.Kim, K.J.Kim. Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase From Corynebacterium Glutamicum. J.Agric.Food Chem. 2023.
ISSN: ESSN 1520-5118
PubMed: 37846083
DOI: 10.1021/ACS.JAFC.3C05180