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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

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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

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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

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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

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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

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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

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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

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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

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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: Thu Dec 28 10:00:35 2023

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