Atomistry » Magnesium » PDB 8jw0-8k9f » 8jzg
Atomistry »
  Magnesium »
    PDB 8jw0-8k9f »
      8jzg »

Magnesium 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:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam, PDB code: 8jzg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8jzg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg506

b:29.8
occ:1.00
 O2A A:3PO502 2.0 37.4 1.0
OD2 A:ASP21 2.3 21.1 1.0
O2B A:3PO502 2.4 40.3 1.0
O3G A:3PO502 2.6 32.5 1.0
CG A:ASP21 3.0 21.4 1.0
OD1 A:ASP21 3.2 20.1 1.0
PA A:3PO502 3.2 38.4 1.0
O3A A:3PO502 3.4 51.7 1.0
PB A:3PO502 3.4 40.8 1.0
O3B A:3PO502 4.0 35.5 1.0
PG A:3PO502 4.0 31.4 1.0
CB A:ARG264 4.0 20.7 1.0
NH1 A:ARG264 4.0 24.2 1.0
O5' A:3PO502 4.0 32.1 1.0
NZ A:LYS265 4.0 27.0 1.0
NE A:ARG264 4.2 21.4 1.0
O1A A:3PO502 4.2 32.2 1.0
CZ A:ARG264 4.4 22.3 1.0
CB A:ASP21 4.5 21.8 1.0
O A:ALA259 4.5 26.0 1.0
CG A:ARG264 4.5 20.7 1.0
O A:ARG264 4.6 21.7 1.0
CE1 A:HIS19 4.7 25.7 1.0
O1G A:3PO502 4.7 28.2 1.0
O1B A:3PO502 4.8 45.8 1.0
K A:K508 4.9 60.6 1.0

Magnesium binding site 2 out of 8 in 8jzg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg507

b:33.1
occ:1.00
 O1B B:3PO502 1.9 39.1 1.0
OD2 A:ASP291 2.2 27.1 1.0
O1G B:3PO502 2.4 43.2 1.0
O1A B:3PO502 2.4 28.6 1.0
O A:HOH603 2.5 27.6 1.0
PG B:3PO502 2.9 40.8 1.0
O3B B:3PO502 2.9 54.1 1.0
PB B:3PO502 2.9 36.7 1.0
O3G B:3PO502 3.0 47.6 1.0
CG A:ASP291 3.1 29.0 1.0
OD1 A:ASP291 3.4 31.2 1.0
O3A B:3PO502 3.6 30.5 1.0
PA B:3PO502 3.6 32.5 1.0
O B:HOH619 3.8 23.2 1.0
NZ A:LYS285 4.1 26.2 1.0
O2B B:3PO502 4.3 27.6 1.0
CA A:GLY280 4.3 21.1 1.0
O2G B:3PO502 4.3 31.4 1.0
O5' B:3PO502 4.4 27.2 1.0
CB A:ASP291 4.5 27.5 1.0
OD2 A:ASP133 4.5 34.8 1.0
NZ B:LYS265 4.6 22.9 1.0
NZ B:LYS180 4.8 30.0 1.0
O2A B:3PO502 4.8 36.4 1.0
MG B:MG506 4.9 31.9 1.0

Magnesium binding site 3 out of 8 in 8jzg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg505

b:41.2
occ:1.00
 O1G A:3PO502 2.1 28.2 1.0
O3A A:3PO502 2.4 51.7 1.0
OD2 B:ASP291 2.5 27.7 1.0
O3B A:3PO502 2.7 35.5 1.0
PB A:3PO502 2.9 40.8 1.0
PG A:3PO502 3.0 31.4 1.0
O1A A:3PO502 3.0 32.2 1.0
O1B A:3PO502 3.3 45.8 1.0
PA A:3PO502 3.4 38.4 1.0
CG B:ASP291 3.6 27.2 1.0
OD2 B:ASP133 3.8 34.8 1.0
O3G A:3PO502 3.8 32.5 1.0
O A:HOH605 4.1 19.4 1.0
OD1 B:ASP291 4.1 26.3 1.0
O2G A:3PO502 4.1 28.4 1.0
O2B A:3PO502 4.3 40.3 1.0
O5' A:3PO502 4.4 32.1 1.0
NZ B:LYS285 4.4 25.2 1.0
O2A A:3PO502 4.4 37.4 1.0
NZ A:LYS180 4.5 29.0 1.0
CB B:ASP291 4.7 29.6 1.0
NZ A:LYS265 4.9 27.0 1.0
CG B:ASP133 4.9 40.2 1.0

Magnesium binding site 4 out of 8 in 8jzg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg506

b:31.9
occ:1.00
 O3B B:3PO502 2.1 54.1 1.0
O5' B:3PO502 2.3 27.2 1.0
OD2 B:ASP21 2.7 22.6 1.0
PG B:3PO502 3.1 40.8 1.0
PB B:3PO502 3.2 36.7 1.0
CG B:ASP21 3.2 20.4 1.0
O2G B:3PO502 3.3 31.4 1.0
PA B:3PO502 3.3 32.5 1.0
O3A B:3PO502 3.3 30.5 1.0
OD1 B:ASP21 3.4 18.6 1.0
NZ B:LYS265 3.6 22.9 1.0
O3G B:3PO502 3.7 47.6 1.0
O2B B:3PO502 3.7 27.6 1.0
O1A B:3PO502 4.1 28.6 1.0
CE1 B:HIS19 4.3 20.9 1.0
O1G B:3PO502 4.4 43.2 1.0
O1B B:3PO502 4.4 39.1 1.0
NH2 B:ARG264 4.5 20.1 1.0
CB B:ASP21 4.5 21.9 1.0
CB B:ARG264 4.5 19.6 1.0
O2A B:3PO502 4.5 36.4 1.0
NE B:ARG264 4.6 20.0 1.0
O B:ALA259 4.7 27.6 1.0
O B:ARG264 4.7 28.1 1.0
CE B:LYS265 4.7 23.1 1.0
CZ B:ARG264 4.8 21.6 1.0
NE2 B:HIS19 4.9 20.0 1.0
MG A:MG507 4.9 33.1 1.0

Magnesium binding site 5 out of 8 in 8jzg

Go back to Magnesium Binding Sites List in 8jzg
Magnesium binding site 5 out of 8 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 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:Mg504

b:33.7
occ:1.00
 O1B C:3PO502 2.0 50.8 1.0
O1G C:3PO502 2.0 36.5 1.0
O2A C:3PO502 2.1 40.1 1.0
OD2 C:ASP21 2.3 34.9 1.0
PB C:3PO502 3.1 45.3 1.0
CG C:ASP21 3.2 34.5 1.0
PG C:3PO502 3.2 40.0 1.0
O3B C:3PO502 3.2 49.6 1.0
OD1 C:ASP21 3.4 30.6 1.0
PA C:3PO502 3.4 42.7 1.0
NH1 C:ARG264 3.6 38.2 1.0
O3A C:3PO502 3.6 38.5 1.0
NZ C:LYS265 4.0 25.6 1.0
O3G C:3PO502 4.0 29.9 1.0
O5' C:3PO502 4.1 42.7 1.0
O2G C:3PO502 4.3 43.5 1.0
O2B C:3PO502 4.4 34.6 1.0
CB C:ARG264 4.4 31.1 1.0
CE1 C:HIS19 4.4 29.6 1.0
O C:ALA259 4.4 31.2 1.0
CB C:ASP21 4.6 31.9 1.0
O1A C:3PO502 4.6 44.0 1.0
CZ C:ARG264 4.7 38.6 1.0
CG C:ARG264 4.8 31.5 1.0
O C:ARG264 4.9 30.1 1.0
CE C:LYS265 5.0 25.4 1.0
K D:K506 5.0 69.5 1.0

Magnesium binding site 6 out of 8 in 8jzg

Go back to Magnesium Binding Sites List in 8jzg
Magnesium binding site 6 out of 8 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 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:Mg505

b:43.4
occ:1.00
 O5' D:3PO502 1.9 37.4 1.0
O3B D:3PO502 2.2 52.8 1.0
OD2 C:ASP291 2.3 34.5 1.0
O2G D:3PO502 2.9 53.1 1.0
O3A D:3PO502 3.0 34.5 1.0
PA D:3PO502 3.0 37.1 1.0
PB D:3PO502 3.1 44.5 1.0
PG D:3PO502 3.2 43.8 1.0
CG C:ASP291 3.3 32.8 1.0
O2B D:3PO502 3.7 37.0 1.0
OD1 C:ASP291 3.7 34.4 1.0
O1A D:3PO502 3.8 34.5 1.0
OD2 C:ASP133 3.9 41.1 1.0
O D:HOH603 3.9 23.3 1.0
O3G D:3PO502 4.1 31.0 1.0
O2A D:3PO502 4.2 36.2 1.0
O1G D:3PO502 4.2 39.0 1.0
NZ C:LYS285 4.2 31.8 1.0
O1B D:3PO502 4.4 40.7 1.0
NZ D:LYS180 4.5 31.9 1.0
O C:HOH614 4.6 35.7 1.0
NZ D:LYS265 4.6 37.8 1.0
CB C:ASP291 4.6 33.8 1.0
MG D:MG505 4.7 26.4 1.0
CA C:GLY280 4.9 30.3 1.0
CG C:ASP133 4.9 39.9 1.0

Magnesium binding site 7 out of 8 in 8jzg

Go back to Magnesium Binding Sites List in 8jzg
Magnesium binding site 7 out of 8 in the C. Glutamicum S-Adenosylmethionine Synthase Co-Crystallized with Adenosine, Triphosphate, and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 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:Mg504

b:43.8
occ:1.00
 O3B C:3PO502 2.1 49.6 1.0
OD2 D:ASP291 2.6 32.0 1.0
O5' C:3PO502 2.7 42.7 1.0
PB C:3PO502 2.8 45.3 1.0
O3A C:3PO502 3.0 38.5 1.0
O2B C:3PO502 3.2 34.6 1.0
PG C:3PO502 3.4 40.0 1.0
PA C:3PO502 3.5 42.7 1.0
CG D:ASP291 3.5 32.5 1.0
O3G C:3PO502 3.7 29.9 1.0
OD1 D:ASP291 3.7 33.1 1.0
OD2 D:ASP133 3.9 35.9 1.0
O1B C:3PO502 4.2 50.8 1.0
O2G C:3PO502 4.2 43.5 1.0
O2A C:3PO502 4.4 40.1 1.0
O1G C:3PO502 4.5 36.5 1.0
NZ C:LYS180 4.5 40.7 1.0
NZ C:LYS265 4.5 25.6 1.0
NZ D:LYS285 4.6 26.5 1.0
O1A C:3PO502 4.7 44.0 1.0
CA D:GLY280 4.8 29.9 1.0
CG D:ASP133 4.9 36.9 1.0
CB D:ASP291 4.9 33.4 1.0

Magnesium binding site 8 out of 8 in 8jzg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 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:Mg505

b:26.4
occ:1.00
 O1B D:3PO502 1.9 40.7 1.0
O1A D:3PO502 2.0 34.5 1.0
O1G D:3PO502 2.1 39.0 1.0
OD2 D:ASP21 2.2 35.2 1.0
PB D:3PO502 2.9 44.5 1.0
O3B D:3PO502 3.1 52.8 1.0
CG D:ASP21 3.2 30.4 1.0
PG D:3PO502 3.2 43.8 1.0
PA D:3PO502 3.2 37.1 1.0
O3A D:3PO502 3.3 34.5 1.0
OD1 D:ASP21 3.5 26.0 1.0
NZ D:LYS265 3.8 37.8 1.0
O5' D:3PO502 4.1 37.4 1.0
O2G D:3PO502 4.2 53.1 1.0
O3G D:3PO502 4.2 31.0 1.0
CE1 D:HIS19 4.2 27.2 1.0
NH2 D:ARG264 4.2 25.6 1.0
O2B D:3PO502 4.3 37.0 1.0
O2A D:3PO502 4.3 36.2 1.0
CB D:ASP21 4.5 29.2 1.0
O D:ALA259 4.6 29.0 1.0
NE2 D:HIS19 4.6 27.5 1.0
CB D:ARG264 4.7 24.2 1.0
CE D:LYS265 4.7 34.7 1.0
MG C:MG505 4.7 43.4 1.0
CZ D:ARG264 4.8 24.7 1.0
NE D:ARG264 4.8 26.2 1.0
O D:ARG264 4.9 32.9 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: Fri Oct 4 13:41:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy