Atomistry » Potassium » PDB 6v8y-6w86 » 6vd2
Atomistry »
  Potassium »
    PDB 6v8y-6w86 »
      6vd2 »

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

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy