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Magnesium in PDB 6vcy: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine, PDB code: 6vcy 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) 49.25 / 1.82
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.280, 69.156, 210.450, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.9

Other elements in 6vcy:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine (pdb code 6vcy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine, PDB code: 6vcy:

Magnesium binding site 1 out of 1 in 6vcy

Go back to Magnesium Binding Sites List in 6vcy
Magnesium binding site 1 out of 1 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


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 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:34.3
occ:1.00
 O A:HOH507 2.0 30.0 1.0
O A:HOH545 2.0 26.5 1.0
O3 A:SO4401 2.0 43.9 1.0
O A:HOH590 2.2 32.8 1.0
O3 A:SO4402 2.3 46.3 1.0
OD2 A:ASP17 2.3 20.5 1.0
O4 A:SO4402 2.9 43.8 1.0
CG A:ASP17 3.1 21.9 1.0
S A:SO4402 3.2 45.6 1.0
S A:SO4401 3.3 61.5 1.0
OD1 A:ASP17 3.4 21.8 1.0
O2 A:SO4401 3.5 61.8 1.0
NZ A:LYS253 3.9 25.1 1.0
O1 A:SO4402 4.0 44.4 1.0
O1 A:SO4401 4.1 48.9 1.0
NH2 A:ARG252 4.2 24.2 1.0
O2 A:SO4402 4.2 46.2 1.0
O4 A:SO4401 4.3 46.9 1.0
CE1 A:HIS15 4.3 23.2 1.0
O A:ALA247 4.4 26.6 1.0
CB A:ASP17 4.5 19.7 1.0
CZ A:ARG252 4.7 22.0 1.0
NE A:ARG252 4.8 21.7 1.0
CE A:LYS253 4.9 24.3 1.0
NE2 A:HIS15 4.9 22.9 1.0
CB A:ARG252 4.9 22.6 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 21:59:10 2024

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