Sodium in PDB 7b1k: Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.

All present enzymatic activity of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.:
2.7.8.8;

The structure of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate., PDB code: 7b1k was solved by O.Yildiz, M.Centola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.00 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.314, 70.758, 95.545, 90, 90, 90
R / Rfree (%)	25.4 / 30.7

The structure of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. (pdb code 7b1k). 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 Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate., PDB code: 7b1k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


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 Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:49.2 occ:1.00 O A:THR53 2.4 47.3 1.0 NAC A:58A301 2.5 31.8 1.0 OG A:SER11 2.5 45.6 1.0 OD1 A:ASP12 3.1 39.5 1.0 OAA A:58A301 3.1 51.6 1.0 CAB A:58A301 3.3 44.7 1.0 OG A:SER55 3.5 32.8 1.0 OG1 A:THR9 3.6 47.3 1.0 CAD A:58A301 3.6 31.7 1.0 C A:THR53 3.6 44.2 1.0 CA A:GLY58 3.7 30.8 1.0 CB A:SER11 3.8 41.0 1.0 CG A:ASP12 3.8 38.4 1.0 N A:SER55 3.8 37.5 1.0 NAE A:58A301 3.9 28.3 1.0 OD2 A:ASP12 3.9 53.0 1.0 CA A:VAL54 4.1 49.0 1.0 C A:VAL54 4.2 46.7 1.0 N A:GLY58 4.2 40.2 1.0 N A:VAL54 4.3 44.2 1.0 CB A:SER55 4.4 47.1 1.0 N A:ASP12 4.4 24.8 1.0 CB A:ALA48 4.5 35.8 1.0 CB A:THR53 4.6 48.0 1.0 OG1 A:THR53 4.6 57.9 1.0 CA A:SER55 4.6 35.7 1.0 C A:GLY58 4.7 45.7 1.0 O A:SER55 4.7 46.5 1.0 NAH A:58A301 4.7 43.2 1.0 CA A:THR53 4.8 44.7 1.0 C A:SER11 4.8 35.6 1.0 CA A:SER11 4.8 34.2 1.0 CB A:THR9 4.8 33.2 1.0 CAF A:58A301 4.9 40.8 1.0 CG2 A:THR9 4.9 56.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


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 Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na310 b:57.7 occ:1.00 OD1 B:ASP12 2.6 46.6 1.0 OG B:SER55 2.8 46.3 1.0 OG1 B:THR9 2.9 63.3 1.0 O B:THR53 2.9 52.4 1.0 OG B:SER11 3.0 42.8 1.0 NAC B:58A301 3.1 36.2 1.0 CG B:ASP12 3.2 41.0 1.0 CG2 B:THR9 3.4 68.7 1.0 OD2 B:ASP12 3.4 54.9 1.0 CB B:THR9 3.7 60.4 1.0 CA B:GLY58 3.7 34.5 1.0 CB B:SER55 3.9 50.4 1.0 OAA B:58A301 4.0 51.9 1.0 NAE B:58A301 4.0 43.6 1.0 CAB B:58A301 4.1 38.6 1.0 CAD B:58A301 4.1 35.3 1.0 C B:THR53 4.1 42.7 1.0 N B:GLY58 4.1 44.2 1.0 N B:SER55 4.2 60.9 1.0 N B:ASP12 4.2 35.4 1.0 CB B:SER11 4.4 36.0 1.0 CB B:ASP12 4.5 45.0 1.0 CB B:THR53 4.5 42.9 1.0 CA B:SER55 4.6 44.0 1.0 CA B:ASP12 4.7 40.7 1.0 CA B:THR9 4.8 62.8 1.0 N B:THR9 4.8 60.7 1.0 C B:SER11 4.9 45.5 1.0 C B:VAL54 4.9 47.2 1.0 OG1 B:THR53 4.9 51.9 1.0 C B:GLY58 4.9 42.0 1.0 O B:SER55 4.9 37.9 1.0 CA B:THR53 4.9 44.8 1.0

M.Centola, H.Betz, O.Yildiz. Crystal Structures of Phosphatidyl Serine Synthase Pss Reveal the Catalytic Mechanism of Cdp-Dag Alcohol O-Phosphatidyl Transferases Nat Commun V. 12 6982 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-27281-W