Sodium in PDB 6scd: Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri

The structure of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri, PDB code: 6scd was solved by A.Bollinger, S.Thies, S.Kobus, A.Hoeppner, S.H.J.Smits, K.-E.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.34 / 1.35
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.526, 98.268, 121.233, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 15.2

The structure of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri (pdb code 6scd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri, PDB code: 6scd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:15.6 occ:1.00 O A:ILE295 2.2 14.4 1.0 O A:THR290 2.4 16.2 1.0 O A:HOH714 2.4 22.6 1.0 O A:HOH693 2.4 23.0 1.0 O A:ASP292 2.5 13.2 1.0 O A:HOH607 2.5 17.8 1.0 C A:ILE295 3.4 12.4 1.0 C A:ASP292 3.5 12.7 1.0 C A:THR290 3.5 15.0 1.0 C A:SER291 3.9 14.7 1.0 O A:SER291 4.0 15.7 1.0 N A:ASP292 4.1 13.9 1.0 N A:ILE295 4.1 12.9 1.0 O A:HOH779 4.2 40.6 1.0 CA A:SER293 4.2 13.3 1.0 CA A:ILE295 4.2 12.6 1.0 N A:SER293 4.2 13.2 1.0 CA A:SER291 4.3 14.8 0.7 CA A:SER291 4.3 15.6 0.3 C A:SER293 4.3 13.1 1.0 N A:SER296 4.4 11.9 1.0 N A:SER291 4.4 14.1 1.0 CA A:ASP292 4.4 13.6 1.0 O A:SER293 4.5 15.2 1.0 CA A:SER296 4.5 13.6 1.0 CA A:THR290 4.5 14.7 1.0 O A:HOH763 4.5 22.1 1.0 CB A:ILE295 4.6 13.2 1.0 CG2 A:THR290 4.8 19.6 1.0 N A:GLN294 5.0 12.7 1.0

Sodium binding site 2 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:17.2 occ:1.00 OG B:SER171 2.9 17.8 1.0 N B:PHE98 3.1 26.1 1.0 N B:MET172 3.2 14.3 1.0 O B:HOH606 3.2 23.8 1.0 CG B:MET172 3.3 17.0 0.7 CG B:MET172 3.3 14.8 0.3 CB B:SER171 3.4 15.1 1.0 SD B:MET172 3.5 16.3 0.3 CB B:PHE98 3.5 36.4 1.0 CB B:MET172 3.5 17.6 0.7 CB B:MET172 3.6 15.1 0.3 CA B:GLY97 3.8 21.2 1.0 CA B:PHE98 3.9 30.7 1.0 SD B:MET172 3.9 24.9 0.7 CA B:MET172 3.9 15.6 0.7 CE B:MET172 3.9 20.9 0.7 CA B:MET172 4.0 15.0 0.3 C B:GLY97 4.0 27.9 1.0 C B:SER171 4.1 13.5 1.0 O B:HOH519 4.2 39.6 1.0 CA B:SER171 4.3 13.6 1.0 NE2 B:HIS249 4.8 16.4 1.0 O B:TRP170 5.0 15.1 1.0 C B:PHE98 5.0 25.9 1.0

Sodium binding site 3 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:20.1 occ:1.00 O B:ALA220 2.8 13.6 1.0 O B:PRO194 2.9 13.9 1.0 O B:HOH607 3.0 13.6 1.0 N B:ALA226 3.1 13.3 1.0 CB B:ALA226 3.3 13.7 1.0 CB B:HIS225 3.4 14.4 1.0 CB B:ALA220 3.6 14.4 1.0 C B:ALA193 3.7 13.9 1.0 C B:ALA220 3.7 12.4 1.0 N B:PRO194 3.7 13.4 1.0 CA B:ALA226 3.8 13.6 1.0 CD B:PRO194 4.0 13.2 1.0 C B:PRO194 4.0 13.2 1.0 CA B:ALA193 4.0 13.5 1.0 O B:ALA193 4.0 13.8 1.0 C B:HIS225 4.1 13.3 1.0 O B:PRO221 4.2 13.7 1.0 CG B:PRO194 4.3 15.0 1.0 CA B:ALA220 4.3 12.9 1.0 CA B:HIS225 4.3 13.8 1.0 C B:PRO221 4.3 12.2 1.0 CA B:VAL222 4.3 12.4 1.0 N B:VAL222 4.4 12.6 1.0 CA B:PRO194 4.4 12.9 1.0 OD2 B:ASP217 4.4 12.6 1.0 CG B:HIS225 4.4 14.9 1.0 CB B:ALA193 4.7 13.7 1.0 N B:PRO221 4.8 13.1 1.0 CG2 B:VAL222 4.8 14.6 1.0 N B:HIS225 5.0 13.9 1.0 CD2 B:HIS225 5.0 14.1 1.0

A.Bollinger, S.Thies, S.Kobus, A.Hoeppner, S.H.J.Smits, C.Coscolin, M.Ferrer, K.-E.Jaeger. A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas Aestusnigri - Structural and Functional Insights Front Microbiol 2020.
ISSN: ESSN 1664-302X
DOI: 10.3389/FMICB.2020.00114