Potassium in PDB 6vd1: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp

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

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp:
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 and Ppnp, PDB code: 6vd1 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) 47.09 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.205, 101.484, 84.334, 90.00, 99.37, 90.00
R / Rfree (%) 14.2 / 17.3

Other elements in 6vd1:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp 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 and Ppnp (pdb code 6vd1). 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 and Ppnp, PDB code: 6vd1:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6vd1

Go back to Potassium Binding Sites List in 6vd1
Potassium binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


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 and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:13.2
occ:1.00
 O2B A:PPK401 2.6 11.0 1.0
OD1 A:ASP246 2.7 13.0 1.0
OE2 B:GLU43 2.8 14.4 1.0
O A:ALA247 2.8 10.4 1.0
O B:HOH631 2.8 14.1 1.0
O A:HOH568 3.1 12.1 1.0
O A:HOH583 3.2 13.2 1.0
O A:HOH556 3.3 19.4 1.0
CG A:ASP246 3.5 12.4 1.0
MG A:MG402 3.7 12.6 1.0
OD2 A:ASP246 3.8 13.6 1.0
C A:ALA247 3.8 10.6 1.0
PB A:PPK401 3.9 11.2 1.0
CD B:GLU43 3.9 12.6 1.0
O B:HOH868 3.9 16.3 1.0
N A:ALA247 4.1 10.2 1.0
O1B A:PPK401 4.2 11.8 1.0
N A:SAM409 4.2 15.2 1.0
CA A:ALA247 4.3 10.5 1.0
CG B:GLU43 4.3 12.7 1.0
CB A:ALA247 4.3 11.7 1.0
NH2 A:ARG252 4.5 13.3 1.0
C A:ASP246 4.7 10.6 1.0
O3A A:PPK401 4.8 11.9 1.0
CB A:ASP246 4.8 11.9 1.0
OE1 B:GLU56 4.8 13.0 1.0
N A:GLY248 4.9 10.4 1.0

Potassium binding site 2 out of 2 in 6vd1

Go back to Potassium Binding Sites List in 6vd1
Potassium binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


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 and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K406

b:13.4
occ:1.00
 OD1 B:ASP246 2.7 12.6 1.0
OE2 A:GLU43 2.8 14.5 1.0
O1B B:PPK401 2.8 11.3 1.0
O A:HOH616 2.8 14.1 1.0
O B:ALA247 2.8 10.7 1.0
O B:HOH586 3.1 11.7 1.0
O B:HOH565 3.2 14.2 1.0
O B:HOH542 3.4 19.6 1.0
CG B:ASP246 3.5 12.9 1.0
MG B:MG404 3.7 13.7 1.0
OD2 B:ASP246 3.8 14.1 1.0
O A:HOH838 3.8 17.1 1.0
C B:ALA247 3.9 9.9 1.0
CD A:GLU43 3.9 12.4 1.0
PB B:PPK401 4.0 11.1 1.0
N B:ALA247 4.0 10.3 1.0
O2B B:PPK401 4.2 11.9 1.0
N B:SAM409 4.3 16.4 1.0
CA B:ALA247 4.3 10.5 1.0
CG A:GLU43 4.3 12.5 1.0
CB B:ALA247 4.3 10.9 1.0
NH2 B:ARG252 4.6 13.3 1.0
C B:ASP246 4.7 10.1 1.0
OE1 A:GLU56 4.8 13.7 1.0
CB B:ASP246 4.8 10.8 1.0
O3A B:PPK401 4.9 11.8 1.0
N B:GLY248 5.0 9.8 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 Dec 14 02:04:44 2020

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