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Potassium 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:

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

Potassium binding site 1 out of 2 in 6vd2

Go back to Potassium Binding Sites List in 6vd2
Potassium binding site 1 out of 2 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 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 S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:46.7
occ:1.00
 OE2 B:GLU43 2.7 32.7 1.0
O A:HOH675 2.8 22.4 1.0
OD1 A:ASP246 2.8 36.5 1.0
O B:HOH580 2.8 39.7 1.0
O A:HOH536 2.8 25.9 1.0
O A:ALA247 2.9 24.4 1.0
O A:HOH613 3.3 30.4 1.0
MG A:MG402 3.5 31.0 1.0
CG A:ASP246 3.5 36.9 1.0
O B:HOH702 3.6 36.5 1.0
CD B:GLU43 3.8 33.3 1.0
OD2 A:ASP246 3.8 35.1 1.0
O A:HOH701 3.9 37.9 1.0
C A:ALA247 4.0 31.9 1.0
CG B:GLU43 4.1 35.6 1.0
N A:ALA247 4.2 33.0 1.0
N A:SAM401 4.3 48.9 1.0
CA A:ALA247 4.5 29.4 1.0
CB A:ALA247 4.5 29.7 1.0
NH2 A:ARG252 4.7 27.5 1.0
OE1 B:GLU56 4.7 43.0 1.0
C A:ASP246 4.7 34.4 1.0
CB A:ASP246 4.8 36.0 1.0
CD1 A:LEU249 4.9 31.1 1.0
OE1 B:GLU43 4.9 33.5 1.0
O2 A:PO4406 4.9 35.1 1.0

Potassium binding site 2 out of 2 in 6vd2

Go back to Potassium Binding Sites List in 6vd2
Potassium binding site 2 out of 2 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 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 S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:40.2
occ:1.00
 OE2 A:GLU43 2.7 35.6 1.0
OD1 B:ASP246 2.8 37.8 1.0
O B:HOH658 2.8 29.1 1.0
O B:ALA247 2.9 31.1 1.0
O B:HOH574 3.0 29.7 1.0
O B:HOH572 3.1 27.6 1.0
O A:HOH508 3.1 29.4 1.0
O A:HOH635 3.5 41.6 1.0
MG B:MG402 3.5 30.7 1.0
CG B:ASP246 3.7 36.2 1.0
CD A:GLU43 3.8 36.9 1.0
C B:ALA247 3.9 30.8 1.0
OD2 B:ASP246 4.0 39.4 1.0
N B:ALA247 4.0 30.1 1.0
O B:HOH719 4.1 49.1 1.0
CG A:GLU43 4.1 37.5 1.0
CA B:ALA247 4.4 30.7 1.0
CB B:ALA247 4.4 32.6 1.0
N B:SAM401 4.5 49.3 1.0
C B:ASP246 4.6 31.7 1.0
OE1 A:GLU56 4.8 42.5 1.0
NH2 B:ARG252 4.9 31.4 1.0
CB B:ASP246 4.9 36.8 1.0
CD1 B:LEU249 4.9 33.0 1.0
OD1 B:ASP17 4.9 26.0 1.0
OE1 A:GLU43 4.9 37.4 1.0
N B:GLY248 5.0 30.7 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: Mon Aug 12 18:00:37 2024

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