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Magnesium in PDB 6vd2: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine, PDB code: 6vd2 was solved by B.Sekula, M.Ruszkowski, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.980, 101.354, 84.708, 90.00, 99.80, 90.00
R / Rfree (%) 19.1 / 24

Other elements in 6vd2:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine (pdb code 6vd2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine, PDB code: 6vd2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vd2

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Magnesium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.0
occ:1.00
 O1 A:PO4405 2.0 37.5 1.0
O2 A:PO4406 2.1 35.1 1.0
O A:HOH675 2.1 22.4 1.0
O A:HOH613 2.1 30.4 1.0
OD2 A:ASP17 2.2 31.5 1.0
O A:HOH536 2.3 25.9 1.0
CG A:ASP17 3.2 27.7 1.0
P A:PO4406 3.4 30.4 1.0
P A:PO4405 3.4 37.0 1.0
OD1 A:ASP17 3.4 30.3 1.0
K A:K404 3.5 46.7 1.0
O4 A:PO4406 3.7 30.5 1.0
NZ A:LYS253 3.8 32.4 1.0
O4 A:PO4405 3.9 42.1 1.0
OD2 A:ASP246 4.1 35.1 1.0
NH2 A:ARG252 4.2 27.5 1.0
O3 A:PO4405 4.2 32.8 1.0
O3 A:PO4406 4.2 30.9 1.0
CE1 A:HIS15 4.3 30.8 1.0
O1 A:PO4406 4.4 36.7 1.0
O2 A:PO4405 4.4 44.5 1.0
O A:ALA247 4.5 24.4 1.0
CB A:ASP17 4.5 28.2 1.0
OE2 B:GLU43 4.5 32.7 1.0
CB A:ARG252 4.7 25.0 1.0
CZ A:ARG252 4.8 26.7 1.0
NE A:ARG252 4.9 27.1 1.0
CG A:ASP246 4.9 36.9 1.0
OD1 A:ASP246 4.9 36.5 1.0
NE2 A:HIS15 4.9 32.8 1.0
CE A:LYS253 5.0 30.8 1.0

Magnesium binding site 2 out of 4 in 6vd2

Go back to Magnesium Binding Sites List in 6vd2
Magnesium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:36.8
occ:1.00
 O3 A:PO4405 2.0 32.8 1.0
O B:HOH538 2.0 32.3 1.0
O3 A:PO4406 2.1 30.9 1.0
O B:HOH598 2.3 27.9 1.0
O A:HOH538 2.3 30.4 1.0
O B:HOH558 2.7 23.0 1.0
P A:PO4406 3.3 30.4 1.0
P A:PO4405 3.5 37.0 1.0
O4 A:PO4406 3.5 30.5 1.0
OD2 B:ASP279 3.6 36.5 1.0
NZ A:LYS253 3.9 32.4 1.0
OD1 B:ASP279 4.0 35.7 1.0
O4 A:PO4405 4.1 42.1 1.0
OD2 B:ASP122 4.1 38.2 1.0
OE1 A:GLU9 4.1 27.3 1.0
O A:HOH561 4.1 26.9 1.0
O2 A:PO4406 4.1 35.1 1.0
O1 A:PO4405 4.1 37.5 1.0
CG B:ASP279 4.2 37.7 1.0
NZ A:LYS169 4.3 30.4 1.0
O A:HOH599 4.3 30.2 1.0
O1 A:PO4406 4.4 36.7 1.0
O2 A:PO4405 4.5 44.5 1.0
CA B:GLY268 4.5 28.7 1.0
O B:HOH621 4.6 33.5 1.0
O B:GLN123 4.7 28.4 1.0
CE A:LYS253 4.7 30.8 1.0
OE2 A:GLU9 4.8 32.3 1.0
CD A:GLU9 4.9 29.4 1.0

Magnesium binding site 3 out of 4 in 6vd2

Go back to Magnesium Binding Sites List in 6vd2
Magnesium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:32.9
occ:1.00
 O3 B:PO4404 1.8 27.6 1.0
O A:HOH579 2.0 31.6 1.0
O A:HOH590 2.1 29.6 1.0
O3 B:PO4405 2.2 31.4 1.0
O B:HOH590 2.2 29.0 1.0
O B:HOH599 2.5 33.9 1.0
P B:PO4404 3.2 29.2 1.0
O1 B:PO4404 3.6 28.6 1.0
OD2 A:ASP279 3.6 37.2 1.0
P B:PO4405 3.6 37.1 1.0
NZ B:LYS253 4.0 29.9 1.0
O2 B:PO4404 4.0 29.4 1.0
OD1 A:ASP279 4.0 36.2 1.0
O A:HOH595 4.1 32.2 1.0
OD2 A:ASP122 4.2 37.5 1.0
NZ B:LYS169 4.2 30.6 1.0
OE1 B:GLU9 4.2 28.8 1.0
O4 B:PO4404 4.2 31.8 1.0
CG A:ASP279 4.2 33.0 1.0
O2 B:PO4405 4.3 30.6 1.0
O1 B:PO4405 4.3 34.7 1.0
O A:HOH585 4.5 22.6 1.0
CA A:GLY268 4.6 28.0 1.0
O4 B:PO4405 4.6 39.2 1.0
O A:HOH526 4.6 36.7 1.0
O A:GLN123 4.8 27.5 1.0
CE B:LYS253 4.8 29.1 1.0
OE2 B:GLU9 4.8 29.4 1.0
CD B:GLU9 5.0 30.1 1.0

Magnesium binding site 4 out of 4 in 6vd2

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Magnesium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.7
occ:1.00
 O2 B:PO4405 2.0 30.6 1.0
O2 B:PO4404 2.1 29.4 1.0
O B:HOH574 2.1 29.7 1.0
OD2 B:ASP17 2.1 27.3 1.0
O B:HOH658 2.2 29.1 1.0
O B:HOH572 2.2 27.6 1.0
CG B:ASP17 3.1 28.1 1.0
P B:PO4405 3.4 37.1 1.0
P B:PO4404 3.4 29.2 1.0
OD1 B:ASP17 3.4 26.0 1.0
K B:K403 3.5 40.2 1.0
O1 B:PO4404 3.6 28.6 1.0
NZ B:LYS253 3.6 29.9 1.0
O1 B:PO4405 3.8 34.7 1.0
O3 B:PO4405 4.0 31.4 1.0
O3 B:PO4404 4.2 27.6 1.0
NH2 B:ARG252 4.2 31.4 1.0
OD2 B:ASP246 4.2 39.4 1.0
CE1 B:HIS15 4.4 32.2 1.0
CB B:ASP17 4.4 28.5 1.0
O4 B:PO4405 4.5 39.2 1.0
O4 B:PO4404 4.5 31.8 1.0
O B:ALA247 4.6 31.1 1.0
OE2 A:GLU43 4.6 35.6 1.0
CB B:ARG252 4.6 25.5 1.0
CZ B:ARG252 4.7 30.4 1.0
CE B:LYS253 4.8 29.1 1.0
OD1 B:ASP246 4.8 37.8 1.0
NE B:ARG252 4.8 29.4 1.0
CG B:ASP246 4.9 36.2 1.0
O B:ARG252 4.9 25.8 1.0

Reference:

B.Sekula, M.Ruszkowski, Z.Dauter. S-Adenosylmethionine Synthases in Plants: Structural Characterization of Type I and II Isoenzymes From Arabidopsis Thaliana and Medicago Truncatula. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32057875
DOI: 10.1016/J.IJBIOMAC.2020.02.100
Page generated: Tue Oct 1 21:59:39 2024

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