Magnesium in PDB 6vcx: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1):
2.5.1.6;

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1), PDB code: 6vcx 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)	48.78 / 1.10
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.722, 68.096, 209.697, 90.00, 90.00, 90.00
R / Rfree (%)	11.1 / 13.5

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) (pdb code 6vcx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1), PDB code: 6vcx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:11.9 occ:1.00 O A:HOH502 2.0 11.8 0.5 O3 A:SO4401 2.0 14.1 1.0 O A:HOH811 2.1 17.9 1.0 O A:HOH590 2.1 12.1 1.0 OD2 A:ASP17 2.2 8.7 1.0 O A:HOH595 2.2 15.4 1.0 O3 A:SO4403 2.2 14.9 0.5 CG A:ASP17 3.1 7.7 1.0 S A:SO4401 3.3 11.8 1.0 OD1 A:ASP17 3.4 7.8 1.0 S A:SO4403 3.4 12.1 0.5 O4 A:SO4401 3.5 16.5 1.0 O2 A:SO4403 3.7 16.9 0.5 NZ A:LYS253 3.8 9.2 1.0 O2 A:SO4401 4.2 13.7 1.0 O1 A:SO4401 4.2 15.1 1.0 NH2 A:ARG252 4.3 9.7 1.0 O4 A:SO4403 4.3 14.7 0.5 CE1 A:HIS15 4.3 8.4 1.0 O A:ALA247 4.4 10.6 1.0 CB A:ASP17 4.4 8.1 1.0 O1 A:SO4403 4.5 9.4 0.5 O A:HOH506 4.6 10.5 0.5 CZ A:ARG252 4.8 8.0 1.0 NE2 A:HIS15 4.9 10.1 1.0 CE A:LYS253 4.9 9.2 1.0 CB A:ARG252 4.9 7.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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 1 (ATMAT1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:25.9 occ:0.80 O A:HOH853 1.8 20.5 0.8 O A:HOH607 1.9 17.1 0.8 O A:HOH997 2.0 44.1 0.8 O A:HOH797 2.0 32.7 0.8 O A:HOH902 2.1 11.2 0.8 OD2 A:ASP64 2.5 17.8 1.0 CG A:ASP64 3.2 12.7 1.0 OD1 A:ASP64 3.2 12.1 1.0 O A:HOH932 4.5 13.8 1.0 O A:HOH540 4.5 28.9 1.0 O A:HOH731 4.5 37.3 1.0 CB A:ASP64 4.6 11.1 1.0 O A:HOH828 4.9 17.5 1.0

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