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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6vcx:

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

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

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 6vcx

Go back to Magnesium Binding Sites List in 6vcx
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 6vcx

Go back to Magnesium Binding Sites List in 6vcx
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

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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