Atomistry » Potassium » PDB 6v8y-6w86 » 6vd1
Atomistry »
  Potassium »
    PDB 6v8y-6w86 »
      6vd1 »

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 Aug 12 18:00:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy