Sodium in PDB 7stu: Crystal Structure of Sulfatase From Pedobacter Yulinensis

The structure of Crystal Structure of Sulfatase From Pedobacter Yulinensis, PDB code: 7stu was solved by A.O'malley, C.R.Schlachter, L.L.Grimes, J.J.Tomashek, A.L.Lee, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.22 / 2.23
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.286, 83.286, 115.793, 90, 90, 120
R / Rfree (%)	17.4 / 22.5

The structure of Crystal Structure of Sulfatase From Pedobacter Yulinensis also contains other interesting chemical elements:

Bromine	(Br)	5 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Sulfatase From Pedobacter Yulinensis (pdb code 7stu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Sulfatase From Pedobacter Yulinensis, PDB code: 7stu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


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 Sulfatase From Pedobacter Yulinensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:37.4 occ:1.00 O A:TYR92 2.3 29.8 1.0 OE1 A:GLU97 2.3 27.3 1.0 O A:PRO89 2.4 30.4 1.0 O A:HOH753 2.4 31.5 1.0 CD A:GLU97 3.1 28.1 1.0 OE2 A:GLU97 3.3 28.8 1.0 C A:PRO89 3.4 29.8 1.0 C A:TYR92 3.4 29.4 1.0 CA A:PRO89 3.8 29.9 1.0 N A:THR94 4.0 26.8 1.0 CA A:VAL93 4.0 28.8 1.0 N A:VAL93 4.1 29.0 1.0 CB A:PRO89 4.2 30.0 1.0 OG1 A:THR94 4.5 25.7 1.0 C A:VAL93 4.5 27.7 1.0 CG A:GLU97 4.5 28.3 1.0 CG2 A:THR94 4.5 25.9 1.0 CA A:TYR92 4.6 29.9 1.0 N A:THR90 4.6 29.4 1.0 N A:TYR92 4.6 29.8 1.0 O A:HIS128 4.8 29.3 1.0 ND1 A:HIS128 4.9 27.4 1.0 CB A:THR94 5.0 26.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


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 Sulfatase From Pedobacter Yulinensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:55.1 occ:1.00 O A:HOH806 2.3 62.3 1.0 OD1 A:ASP80 2.3 42.4 1.0 O A:THR83 2.3 29.0 1.0 O A:HOH734 2.7 53.9 1.0 O A:ASP80 3.0 35.1 1.0 C A:THR83 3.5 28.5 1.0 CG A:ASP80 3.6 39.5 1.0 C A:ASP80 3.9 35.6 1.0 CA A:ASP80 4.1 36.2 1.0 CA A:ASP84 4.2 28.2 1.0 N A:ASP84 4.2 28.5 1.0 CG2 A:THR83 4.3 28.4 1.0 CB A:ASP80 4.4 37.7 1.0 OD2 A:ASP80 4.4 43.7 1.0 CB A:ASP117 4.6 34.8 1.0 CA A:THR83 4.7 28.7 1.0 O A:HOH773 4.7 44.5 1.0 C A:ASP84 4.8 28.1 1.0 O A:HOH738 4.9 49.9 1.0 N A:THR83 4.9 29.4 1.0 O A:HOH612 4.9 41.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Sulfatase From Pedobacter Yulinensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:38.0 occ:1.00 O A:HOH842 2.1 46.1 1.0 O A:PHE147 2.3 38.9 1.0 O A:PRO149 2.4 37.2 1.0 OD2 A:ASP145 2.5 35.1 1.0 OD1 A:ASP145 2.5 35.7 1.0 CG A:ASP145 2.8 34.2 1.0 C A:PRO149 3.4 37.8 1.0 C A:PHE147 3.5 38.2 1.0 N A:PRO149 4.1 38.8 1.0 N A:TYR150 4.1 37.0 1.0 C A:PHE148 4.2 38.7 1.0 CA A:TYR150 4.2 36.4 1.0 CB A:ASP145 4.3 33.5 1.0 N A:SER151 4.3 35.8 1.0 CA A:PRO149 4.3 38.3 1.0 CA A:PHE147 4.3 37.9 1.0 N A:PHE147 4.4 36.1 1.0 O A:PHE148 4.4 38.8 1.0 CB A:PHE147 4.5 39.6 1.0 N A:PHE148 4.5 38.7 1.0 CD A:PRO149 4.6 39.4 1.0 CA A:PHE148 4.7 39.0 1.0 O A:HOH860 4.7 49.5 1.0 C A:TYR150 4.8 36.0 1.0 CG A:PRO149 4.8 39.0 1.0

C.R.Schlachter, A.O'malley, L.L.Grimes, J.J.Tomashek, M.Chruszcz, L.A.Lee. Purification, Characterization, and Structural Studies of A Sulfatase From Pedobacter Yulinensis . Molecules V. 27 2021.
ISSN: ESSN 1420-3049
PubMed: 35011319
DOI: 10.3390/MOLECULES27010087