Potassium in PDB 8jzg: C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam

Enzymatic activity of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam

All present enzymatic activity of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam:
2.5.1.6;

Protein crystallography data

The structure of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam, PDB code: 8jzg 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) 32.63 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.311, 116.806, 116.314, 90, 103.31, 90
R / Rfree (%) 19.4 / 26

Other elements in 8jzg:

The structure of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam (pdb code 8jzg). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam, PDB code: 8jzg:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8jzg

Go back to Potassium Binding Sites List in 8jzg
Potassium binding site 1 out of 4 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K508

b:60.6
occ:1.00
 OD1 A:ASP258 3.1 68.5 1.0
O2B A:3PO502 3.2 40.3 1.0
OE2 B:GLU60 3.4 64.5 1.0
O A:ALA259 3.8 26.0 1.0
O1B A:3PO502 4.0 45.8 1.0
N A:ALA259 4.1 33.1 1.0
OE1 B:GLU47 4.1 45.7 1.0
PB A:3PO502 4.1 40.8 1.0
CG A:ASP258 4.3 54.0 1.0
CD B:GLU60 4.4 50.1 1.0
CB B:ALA45 4.5 24.2 1.0
C A:ASP258 4.5 41.8 1.0
CA A:ASP258 4.6 45.5 1.0
C A:ALA259 4.7 25.9 1.0
OE1 B:GLU60 4.8 49.9 1.0
CA A:ALA259 4.8 28.4 1.0
O3B A:3PO502 4.8 35.5 1.0
CB A:ASP258 4.9 46.5 1.0
CB A:ALA259 4.9 27.8 1.0
MG A:MG506 4.9 29.8 1.0

Potassium binding site 2 out of 4 in 8jzg

Go back to Potassium Binding Sites List in 8jzg
Potassium binding site 2 out of 4 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K509

b:64.2
occ:1.00
 OD1 B:ASP258 3.2 57.3 1.0
OE2 A:GLU60 3.5 43.4 1.0
O2A B:3PO502 3.5 36.4 1.0
O B:ALA259 3.6 27.6 1.0
O5' B:3PO502 3.7 27.2 1.0
N B:ALA259 3.8 32.7 1.0
OE1 A:GLU47 4.2 44.3 1.0
PA B:3PO502 4.2 32.5 1.0
CG B:ASP258 4.4 53.0 1.0
C B:ASP258 4.4 43.8 1.0
CA B:ALA259 4.5 28.5 1.0
C B:ALA259 4.5 27.0 1.0
CA B:ASP258 4.5 49.6 1.0
CB B:ALA259 4.5 26.4 1.0
CB A:ALA45 4.6 25.6 1.0
CD A:GLU60 4.6 49.0 1.0
CB B:ASP258 5.0 48.0 1.0
O3A B:3PO502 5.0 30.5 1.0

Potassium binding site 3 out of 4 in 8jzg

Go back to Potassium Binding Sites List in 8jzg
Potassium binding site 3 out of 4 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K506

b:68.6
occ:1.00
 OD1 D:ASP258 2.9 78.4 1.0
OE2 C:GLU60 3.1 59.3 1.0
O1B D:3PO502 3.7 40.7 1.0
CG D:ASP258 3.7 71.1 1.0
O D:ALA259 3.9 29.0 1.0
N D:ALA259 3.9 36.0 1.0
O2B D:3PO502 4.1 37.0 1.0
OD2 D:ASP258 4.3 78.8 1.0
CD C:GLU60 4.3 55.0 1.0
CA D:ASP258 4.3 51.8 1.0
OE1 C:GLU47 4.4 37.9 1.0
PB D:3PO502 4.4 44.5 1.0
C D:ASP258 4.5 44.7 1.0
CB C:ALA45 4.5 27.2 1.0
O C:HOH648 4.6 42.1 1.0
CB D:ASP258 4.6 58.0 1.0
CA D:ALA259 4.7 32.6 1.0
CB D:ALA259 4.7 29.2 1.0
C D:ALA259 4.7 34.4 1.0
CG C:GLU60 4.9 47.0 1.0

Potassium binding site 4 out of 4 in 8jzg

Go back to Potassium Binding Sites List in 8jzg
Potassium binding site 4 out of 4 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K506

b:69.5
occ:1.00
 OE1 D:GLU60 3.4 52.6 1.0
O1A C:3PO502 3.4 44.0 1.0
OD1 C:ASP258 3.6 71.2 1.0
O2A C:3PO502 3.7 40.1 1.0
O C:ALA259 3.7 31.2 1.0
N C:ALA259 3.9 38.5 1.0
OE1 D:GLU47 4.1 43.6 1.0
PA C:3PO502 4.1 42.7 1.0
CG C:ASP258 4.3 66.3 1.0
C C:ASP258 4.4 49.5 1.0
CD D:GLU60 4.4 53.0 1.0
CA C:ASP258 4.5 55.6 1.0
CA C:ALA259 4.6 35.6 1.0
C C:ALA259 4.6 32.6 1.0
CB C:ALA259 4.6 34.7 1.0
CB D:ALA45 4.7 32.3 1.0
OE2 D:GLU60 4.8 49.0 1.0
OD2 C:ASP258 4.9 56.4 1.0
MG C:MG504 5.0 33.7 1.0

Reference:

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
Page generated: Tue Aug 13 00:10:07 2024

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