Atomistry » Potassium » PDB 8jxp-8q0j » 8jzg
Atomistry »
  Potassium »
    PDB 8jxp-8q0j »
      8jzg »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy