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Sodium in PDB 6czz: Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate:
2.6.1.52;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate, PDB code: 6czz 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) 44.40 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 189.668, 53.288, 137.921, 90.00, 91.91, 90.00
R / Rfree (%) 18.1 / 20.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate (pdb code 6czz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate, PDB code: 6czz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6czz

Go back to Sodium Binding Sites List in 6czz
Sodium binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:29.6
occ:0.50
 O A:HOH714 2.2 28.0 1.0
O A:HOH923 2.5 36.2 1.0
O A:ALA93 2.7 17.8 1.0
C A:ALA93 3.6 16.9 1.0
O A:HOH940 3.7 23.0 0.5
OD1 A:ASP94 4.0 27.0 1.0
O A:HOH892 4.1 22.6 1.0
CB A:ALA93 4.1 16.2 1.0
CA A:ALA93 4.4 16.2 1.0
N A:ASP94 4.5 17.4 1.0
CA A:ASP94 4.6 20.2 1.0
O A:HOH615 4.7 42.7 1.0
CG A:ASP94 4.8 25.1 1.0
O A:HOH850 4.8 23.1 1.0
O A:ASN97 4.9 22.8 1.0

Sodium binding site 2 out of 2 in 6czz

Go back to Sodium Binding Sites List in 6czz
Sodium binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Arabidopsis Thaliana Phosphoserine Aminotransferase Isoform 1 (ATPSAT1) in Complex with Plp- Phosphoserine Geminal Diamine Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:34.2
occ:0.50
 O C:HOH635 2.3 38.8 1.0
O C:HOH885 2.5 42.5 1.0
O C:ALA93 2.7 25.0 1.0
O C:HOH910 3.5 23.0 0.5
C C:ALA93 3.7 25.4 1.0
OD1 C:ASP94 4.0 30.5 1.0
O C:HOH834 4.1 24.0 1.0
CB C:ALA93 4.2 24.8 1.0
CA C:ALA93 4.4 26.3 1.0
N C:ASP94 4.5 23.6 1.0
O C:HOH620 4.5 41.9 1.0
CA C:ASP94 4.6 24.0 1.0
O C:HOH841 4.7 34.6 1.0
CG C:ASP94 4.8 27.9 1.0
O C:ASN97 4.8 25.8 1.0

Reference:

B.Sekula, M.Ruszkowski, Z.Dauter. Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) Fromarabidopsis Thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. Front Plant Sci V. 9 876 2018.
ISSN: ESSN 1664-462X
PubMed: 30034403
DOI: 10.3389/FPLS.2018.00876
Page generated: Tue Oct 8 06:52:18 2024

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