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Potassium in PDB 6vd0: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp

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

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

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp, PDB code: 6vd0 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) 39.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.941, 84.721, 119.503, 90.00, 95.67, 90.00
R / Rfree (%) 22.2 / 25.1

Other elements in 6vd0:

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

Magnesium (Mg) 9 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp (pdb code 6vd0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp, PDB code: 6vd0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6vd0

Go back to Potassium Binding Sites List in 6vd0
Potassium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:23.7
occ:1.00
 OD1 A:ASP246 2.7 19.0 1.0
O2B A:APC401 2.8 19.5 1.0
O B:HOH604 2.8 17.7 1.0
O A:ALA247 2.8 19.2 1.0
OE2 B:GLU43 2.9 25.6 1.0
O A:HOH613 3.1 18.8 1.0
O A:HOH513 3.3 19.3 1.0
O A:HOH637 3.5 17.4 1.0
CG A:ASP246 3.5 20.1 1.0
O B:HOH678 3.6 23.2 1.0
MG A:MG404 3.8 21.0 1.0
OD2 A:ASP246 3.9 21.1 1.0
C A:ALA247 3.9 18.2 1.0
N A:ALA247 3.9 20.3 1.0
PB A:APC401 4.0 21.0 1.0
CD B:GLU43 4.0 25.8 1.0
N B:MET402 4.2 24.6 1.0
CA A:ALA247 4.2 19.6 1.0
O1B A:APC401 4.2 21.3 1.0
CB A:ALA247 4.3 19.1 1.0
CG B:GLU43 4.4 26.9 1.0
C A:ASP246 4.5 20.8 1.0
OE1 B:GLU56 4.6 26.5 1.0
CB A:ASP246 4.7 19.8 1.0
C3A A:APC401 4.7 19.9 1.0
NH2 A:ARG252 4.7 19.7 1.0
CA A:ASP246 4.8 20.8 1.0

Potassium binding site 2 out of 4 in 6vd0

Go back to Potassium Binding Sites List in 6vd0
Potassium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:23.4
occ:1.00
 O2B B:APC401 2.6 21.7 1.0
OD1 B:ASP246 2.7 20.8 1.0
O A:HOH683 2.7 18.0 1.0
OE2 A:GLU43 2.8 21.2 1.0
O B:ALA247 2.9 19.6 1.0
O B:HOH574 3.0 13.4 1.0
O B:HOH512 3.2 21.2 1.0
O B:HOH571 3.5 16.7 1.0
CG B:ASP246 3.5 22.0 1.0
MG B:MG403 3.7 17.9 1.0
O A:HOH697 3.7 28.4 1.0
OD2 B:ASP246 3.8 23.1 1.0
CD A:GLU43 3.8 20.4 1.0
PB B:APC401 3.9 23.2 1.0
C B:ALA247 3.9 18.9 1.0
N B:ALA247 4.0 19.5 1.0
O1B B:APC401 4.2 21.2 1.0
CG A:GLU43 4.3 21.1 1.0
CA B:ALA247 4.3 18.5 1.0
CB B:ALA247 4.3 18.1 1.0
N A:MET402 4.3 29.3 1.0
C B:ASP246 4.6 21.6 1.0
C3A B:APC401 4.6 19.2 1.0
OE1 A:GLU56 4.7 23.9 1.0
CB B:ASP246 4.7 22.8 1.0
NH2 B:ARG252 4.8 24.0 1.0
CA B:ASP246 4.9 23.3 1.0
OE1 A:GLU43 4.9 21.2 1.0
O2A B:APC401 4.9 19.6 1.0

Potassium binding site 3 out of 4 in 6vd0

Go back to Potassium Binding Sites List in 6vd0
Potassium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K407

b:32.4
occ:1.00
 OD1 C:ASP246 2.7 29.1 1.0
O1B C:APC402 2.7 20.1 1.0
O D:HOH648 2.8 23.0 1.0
OE2 D:GLU43 2.9 25.8 1.0
O C:ALA247 3.0 25.2 1.0
O C:HOH579 3.0 26.8 1.0
O C:HOH504 3.1 26.2 1.0
O D:HOH569 3.2 35.5 1.0
CG C:ASP246 3.4 28.4 1.0
O C:HOH653 3.6 24.0 1.0
OD2 C:ASP246 3.7 27.4 1.0
MG C:MG405 3.7 25.6 1.0
PB C:APC402 3.9 23.9 1.0
C C:ALA247 4.0 26.1 1.0
CD D:GLU43 4.0 25.2 1.0
N C:ALA247 4.1 26.3 1.0
O2B C:APC402 4.1 24.9 1.0
N D:MET402 4.2 29.7 1.0
CA C:ALA247 4.4 26.7 1.0
CG D:GLU43 4.4 27.2 1.0
CB C:ALA247 4.4 26.4 1.0
C C:ASP246 4.6 28.3 1.0
C3A C:APC402 4.6 24.0 1.0
OE1 D:GLU56 4.7 26.2 1.0
CB C:ASP246 4.7 28.0 1.0
NH2 C:ARG252 4.7 27.1 1.0
O1A C:APC402 4.8 20.7 1.0
CA C:ASP246 4.9 28.1 1.0

Potassium binding site 4 out of 4 in 6vd0

Go back to Potassium Binding Sites List in 6vd0
Potassium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K404

b:26.7
occ:1.00
 O1B D:APC401 2.6 25.5 1.0
OE2 C:GLU43 2.7 30.0 1.0
OD1 D:ASP246 2.9 29.2 1.0
O D:ALA247 2.9 21.8 1.0
O C:HOH645 3.0 22.1 1.0
O D:HOH601 3.0 20.4 1.0
O D:HOH566 3.4 28.8 1.0
O C:HOH529 3.4 27.6 1.0
O D:HOH617 3.4 28.1 1.0
CG D:ASP246 3.6 29.9 1.0
PB D:APC401 3.8 25.2 1.0
MG D:MG403 3.8 27.9 1.0
OD2 D:ASP246 3.8 35.6 1.0
CD C:GLU43 3.8 28.7 1.0
C D:ALA247 3.9 23.3 1.0
O2B D:APC401 4.0 25.6 1.0
N D:ALA247 4.1 26.0 1.0
CG C:GLU43 4.2 28.0 1.0
CB D:ALA247 4.3 24.1 1.0
CA D:ALA247 4.3 25.3 1.0
N C:MET403 4.4 27.5 1.0
C D:ASP246 4.7 28.6 1.0
OE1 C:GLU56 4.7 27.4 1.0
C3A D:APC401 4.7 23.7 1.0
NH2 D:ARG252 4.7 24.2 1.0
O1A D:APC401 4.8 21.4 1.0
CB D:ASP246 4.9 29.0 1.0
OE1 C:GLU43 5.0 27.3 1.0
CA D:ASP246 5.0 27.5 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: Sat Aug 9 12:27:03 2025

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