Sodium in PDB 8jzi: Mutant S-Adenosylmethionine Synthase From C. Glutamicum

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

The structure of Mutant S-Adenosylmethionine Synthase From C. Glutamicum, PDB code: 8jzi 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)	31.55 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.404, 125.436, 116.31, 90, 128.91, 90
R / Rfree (%)	18.2 / 21.8

The binding sites of Sodium atom in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum (pdb code 8jzi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum, PDB code: 8jzi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutant S-Adenosylmethionine Synthase From C. Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:8.7 occ:1.00 O A:HOH615 2.5 15.8 1.0 O A:HOH765 2.5 22.7 1.0 OE1 A:GLU333 2.5 16.2 1.0 OD2 B:ASP191 2.5 17.4 1.0 O A:HOH828 2.6 24.3 1.0 O B:HOH743 2.6 17.9 1.0 OD1 B:ASP191 2.6 16.7 1.0 OE2 A:GLU333 2.7 15.9 1.0 CG B:ASP191 2.9 18.1 1.0 CD A:GLU333 2.9 14.4 1.0 OD2 A:ASP344 4.2 20.1 1.0 O A:HOH729 4.3 25.6 1.0 CB B:ASP191 4.4 17.4 1.0 CG A:GLU333 4.4 13.3 1.0 NH1 B:ARG8 4.5 17.9 1.0 O A:HOH681 4.5 33.5 1.0 NH2 B:ARG8 4.5 18.6 1.0 O B:ALA189 4.7 20.8 1.0 O A:HOH651 4.7 17.2 1.0 O B:HOH752 4.7 16.6 1.0 O B:HOH655 4.8 17.6 1.0 O B:HOH930 4.8 27.0 1.0 N A:PHE335 4.9 14.5 1.0 OD1 A:ASP336 4.9 30.4 1.0 CZ B:ARG8 5.0 18.6 1.0

Sodium binding site 2 out of 4 in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mutant S-Adenosylmethionine Synthase From C. Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:6.4 occ:1.00 O B:HOH642 2.4 19.9 1.0 OE2 B:GLU333 2.4 15.4 1.0 O A:HOH753 2.5 18.0 1.0 O B:HOH851 2.5 22.1 1.0 OD2 A:ASP191 2.5 14.8 1.0 OD1 A:ASP191 2.6 15.1 1.0 O B:HOH900 2.6 17.7 1.0 OE1 B:GLU333 2.6 15.7 1.0 CD B:GLU333 2.8 13.3 1.0 CG A:ASP191 2.9 14.9 1.0 O B:HOH789 4.2 19.9 1.0 OD2 B:ASP344 4.3 16.9 1.0 NH1 A:ARG8 4.3 14.7 1.0 CG B:GLU333 4.4 12.2 1.0 CB A:ASP191 4.4 15.2 1.0 NH2 A:ARG8 4.6 13.4 1.0 O A:HOH693 4.6 13.7 1.0 O A:ALA189 4.6 15.6 1.0 O A:HOH696 4.8 17.6 1.0 O B:HOH765 4.8 18.3 1.0 O A:HOH913 4.9 28.7 1.0 CZ A:ARG8 4.9 13.2 1.0 N B:PHE335 4.9 13.9 1.0

Sodium binding site 3 out of 4 in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mutant S-Adenosylmethionine Synthase From C. Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:10.7 occ:1.00 O C:HOH725 2.3 17.7 1.0 OD1 C:ASP191 2.5 17.7 1.0 O C:HOH817 2.5 28.3 1.0 O D:HOH657 2.5 20.5 1.0 OE2 D:GLU333 2.5 18.4 1.0 OD2 C:ASP191 2.6 16.7 1.0 OE1 D:GLU333 2.7 18.7 1.0 O D:HOH622 2.7 20.1 1.0 CG C:ASP191 2.9 15.7 1.0 CD D:GLU333 2.9 17.4 1.0 OD2 D:ASP344 4.3 20.9 1.0 O D:HOH624 4.3 31.3 1.0 NH1 C:ARG8 4.3 15.0 1.0 CB C:ASP191 4.4 15.9 1.0 CG D:GLU333 4.5 15.5 1.0 O C:ALA189 4.5 19.4 1.0 NH2 C:ARG8 4.6 15.2 1.0 O C:HOH727 4.6 18.5 1.0 O D:HOH658 4.7 18.1 1.0 O C:HOH685 4.8 26.7 1.0 CZ C:ARG8 4.9 13.6 1.0

Sodium binding site 4 out of 4 in the Mutant S-Adenosylmethionine Synthase From C. Glutamicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mutant S-Adenosylmethionine Synthase From C. Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:16.0 occ:1.00 O C:HOH825 2.3 36.0 1.0 O C:HOH809 2.4 30.9 1.0 OD1 D:ASP191 2.4 22.6 1.0 O D:HOH716 2.5 21.6 1.0 OE2 C:GLU333 2.5 22.2 1.0 O C:HOH634 2.5 24.7 1.0 OD2 D:ASP191 2.6 29.2 1.0 OE1 C:GLU333 2.7 20.2 1.0 CG D:ASP191 2.9 25.7 1.0 CD C:GLU333 2.9 25.4 1.0 NH1 D:ARG8 4.3 24.9 1.0 CB D:ASP191 4.4 24.5 1.0 OD2 C:ASP344 4.4 25.1 1.0 CG C:GLU333 4.4 20.7 1.0 O C:HOH655 4.5 22.9 1.0 NH2 D:ARG8 4.6 25.7 1.0 O D:ALA189 4.6 26.9 1.0 CZ D:ARG8 4.9 27.4 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