Sodium in PDB 7z6b: Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes

The structure of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes, PDB code: 7z6b was solved by S.Weigert, B.Hoecker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.70 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.82, 72.61, 72.76, 119.78, 91.64, 91.82
R / Rfree (%)	10 / 12.6

The structure of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes (pdb code 7z6b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes, PDB code: 7z6b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:19.5 occ:1.00 O A:HOH652 2.4 26.8 1.0 O A:VAL287 2.4 12.8 1.0 O A:ASP282 2.4 21.3 1.0 O A:HOH557 2.4 21.1 1.0 O A:HOH634 2.4 23.4 1.0 O A:SER284 2.4 19.9 1.0 HA A:SER288 3.3 11.7 1.0 C A:SER284 3.4 20.8 1.0 HA A:LEU285 3.4 20.1 0.5 HA A:LEU285 3.4 20.1 0.5 C A:ASP282 3.4 20.4 1.0 C A:VAL287 3.4 11.7 1.0 HB2 A:ASP282 3.5 22.1 1.0 H A:VAL287 3.6 11.9 1.0 HA A:ASP282 3.6 19.9 1.0 CA A:ASP282 4.0 19.9 1.0 CA A:LEU285 4.0 20.2 0.5 CA A:LEU285 4.0 20.1 0.5 N A:LEU285 4.1 22.1 1.0 CA A:SER288 4.1 11.7 1.0 CB A:ASP282 4.2 22.1 1.0 N A:SER288 4.2 11.4 1.0 C A:SER283 4.2 24.0 1.0 N A:SER284 4.2 21.8 1.0 N A:VAL287 4.2 11.9 1.0 HB A:VAL287 4.3 12.3 1.0 C A:LEU285 4.3 18.6 1.0 CA A:VAL287 4.4 12.0 1.0 O A:SER283 4.4 26.7 1.0 O A:HOH707 4.4 31.1 1.0 CA A:SER284 4.4 19.5 1.0 N A:SER283 4.5 22.8 1.0 H A:SER284 4.5 21.8 1.0 O A:LEU285 4.5 19.2 1.0 HA A:SER283 4.5 22.4 1.0 C A:SER288 4.5 12.3 1.0 O A:SER288 4.6 15.3 1.0 HB3 A:ASP282 4.6 22.1 1.0 CA A:SER283 4.7 22.4 1.0 H A:LEU285 4.8 22.1 0.5 H A:LEU285 4.8 22.1 0.5 HD12 A:LEU285 4.8 24.2 0.5 CB A:VAL287 4.9 12.3 1.0 N A:ARG286 4.9 16.5 1.0 HB2 A:ALA237 5.0 12.1 1.0

Sodium binding site 2 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:17.1 occ:1.00 O A:ARG61 2.3 21.0 1.0 O A:ALA63 2.4 17.3 1.0 O A:HOH642 2.4 27.7 1.0 O A:PHE66 2.4 12.1 1.0 O A:HOH550 2.5 19.0 1.0 O A:HOH509 2.6 20.1 1.0 H A:PHE66 3.4 11.0 1.0 C A:ARG61 3.5 17.9 1.0 C A:ALA63 3.6 17.3 1.0 C A:PHE66 3.6 10.3 1.0 HA2 A:GLY67 3.7 10.4 1.0 HG3 A:ARG61 3.7 24.9 0.2 OD1 A:ASN117 3.9 13.8 1.0 H A:GLY65 3.9 12.6 1.0 N A:ALA63 4.0 16.3 1.0 C A:LEU62 4.0 19.6 1.0 HA A:LEU62 4.0 21.6 1.0 HA A:ARG61 4.1 19.1 0.8 HA A:ARG61 4.1 19.1 0.2 N A:PHE66 4.1 11.0 1.0 H A:ALA63 4.2 16.3 1.0 HG2 A:ARG61 4.3 24.9 0.2 CA A:ALA63 4.3 17.2 1.0 HB3 A:ARG61 4.3 22.1 0.8 O A:LEU62 4.3 21.5 1.0 HB3 A:ALA63 4.3 18.1 1.0 CA A:ARG61 4.3 18.3 0.8 CA A:ARG61 4.3 19.1 0.2 CA A:LEU62 4.4 21.6 1.0 N A:LEU62 4.4 18.7 1.0 CG A:ARG61 4.4 24.9 0.2 N A:GLY65 4.4 12.6 1.0 HA A:ARG64 4.4 17.8 0.5 CA A:GLY67 4.4 10.4 1.0 N A:GLY67 4.4 10.1 1.0 CA A:PHE66 4.5 10.4 1.0 HA A:ARG64 4.5 17.8 0.5 N A:ARG64 4.6 18.0 1.0 H A:GLY68 4.6 10.1 1.0 CA A:ARG64 4.8 17.9 0.5 C A:ARG64 4.9 14.5 1.0 CA A:ARG64 4.9 17.8 0.5 CB A:ALA63 4.9 18.1 1.0 CB A:ARG61 4.9 22.9 0.8 HA A:PHE66 4.9 10.4 1.0 CB A:ARG61 5.0 22.1 0.2

Sodium binding site 3 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:23.4 occ:1.00 O B:HOH639 2.3 31.2 1.0 O B:VAL287 2.4 17.0 1.0 O B:ASP282 2.4 26.4 1.0 O B:SER284 2.4 24.7 1.0 O B:HOH512 2.5 24.6 1.0 O B:HOH627 2.5 28.8 1.0 HA B:SER288 3.4 13.0 1.0 C B:SER284 3.4 23.3 1.0 C B:ASP282 3.5 24.4 1.0 C B:VAL287 3.5 13.7 1.0 HB2 B:ASP282 3.6 25.1 1.0 H B:VAL287 3.6 14.7 1.0 HA B:LEU285 3.7 23.8 1.0 HA B:ASP282 3.7 21.8 1.0 CA B:ASP282 4.1 21.8 1.0 CA B:SER288 4.2 13.0 1.0 C B:SER283 4.2 28.7 1.0 N B:LEU285 4.2 24.2 1.0 N B:SER284 4.2 23.8 1.0 N B:SER288 4.2 12.3 1.0 N B:VAL287 4.2 14.7 1.0 CA B:LEU285 4.3 23.8 1.0 CB B:ASP282 4.3 25.1 1.0 HB B:VAL287 4.3 15.5 1.0 O B:SER283 4.4 30.0 1.0 C B:LEU285 4.4 21.3 1.0 CA B:VAL287 4.4 14.1 1.0 CA B:SER284 4.4 25.1 1.0 O B:LEU285 4.5 21.9 1.0 H B:SER284 4.5 23.8 1.0 HA B:SER283 4.5 27.9 1.0 N B:SER283 4.5 27.5 1.0 C B:SER288 4.6 13.6 1.0 O B:SER288 4.6 16.6 1.0 CA B:SER283 4.7 27.9 1.0 HB3 B:ASP282 4.7 25.1 1.0 O B:HOH699 4.8 46.7 1.0 O B:HOH679 4.9 34.5 1.0 CB B:VAL287 4.9 15.5 1.0 HB2 B:ALA237 4.9 12.9 1.0 HB3 B:SER284 5.0 23.8 1.0 N B:ARG286 5.0 17.5 1.0 H B:LEU285 5.0 24.2 1.0

Sodium binding site 4 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:16.6 occ:1.00 O B:ARG61 2.3 20.8 1.0 O B:HOH631 2.3 31.4 1.0 O B:ALA63 2.4 17.2 1.0 O B:PHE66 2.4 11.4 1.0 O B:HOH502 2.5 19.7 1.0 O B:HOH557 2.6 18.5 1.0 H B:PHE66 3.4 10.4 1.0 C B:ARG61 3.5 18.4 1.0 C B:PHE66 3.6 9.9 1.0 C B:ALA63 3.6 16.8 1.0 HA2 B:GLY67 3.8 10.2 1.0 H B:GLY65 3.8 12.4 1.0 OD1 B:ASN117 4.0 15.0 1.0 HA B:ARG61 4.0 18.9 0.8 HA B:ARG61 4.0 18.9 0.2 N B:ALA63 4.0 18.8 1.0 C B:LEU62 4.0 20.0 1.0 N B:PHE66 4.0 10.4 1.0 HA B:LEU62 4.1 22.0 1.0 H B:ALA63 4.2 18.8 1.0 HB3 B:ARG61 4.2 21.5 0.2 HB3 B:ARG61 4.3 21.5 0.8 CA B:ARG61 4.3 19.1 0.8 CA B:ARG61 4.3 18.9 0.2 O B:LEU62 4.3 24.5 1.0 N B:GLY65 4.4 12.4 1.0 N B:LEU62 4.4 20.1 1.0 CA B:ALA63 4.4 17.5 1.0 HB3 B:ALA63 4.4 19.1 1.0 CA B:LEU62 4.4 22.0 1.0 CA B:PHE66 4.5 9.8 1.0 N B:GLY67 4.5 9.2 1.0 CA B:GLY67 4.5 10.2 1.0 HA B:ARG64 4.5 16.7 0.3 HA B:ARG64 4.6 16.7 0.7 N B:ARG64 4.7 17.6 1.0 H B:GLY68 4.7 10.8 1.0 CB B:ARG61 4.8 21.5 0.2 CB B:ARG61 4.9 23.4 0.8 C B:ARG64 4.9 14.1 1.0 HA B:PHE66 4.9 9.9 1.0 CA B:ARG64 4.9 17.1 0.7 CA B:ARG64 4.9 16.7 0.3 CB B:ALA63 5.0 19.1 1.0 C B:GLY65 5.0 11.4 1.0

Sodium binding site 5 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:16.7 occ:1.00 O C:HOH629 2.4 23.0 1.0 O C:ASP282 2.4 17.5 1.0 O C:VAL287 2.4 13.3 1.0 O C:HOH559 2.5 19.1 1.0 O C:SER284 2.5 16.1 1.0 O C:HOH630 2.5 24.3 1.0 HA C:SER288 3.4 12.1 1.0 C C:ASP282 3.5 16.1 1.0 C C:VAL287 3.5 12.8 1.0 C C:SER284 3.5 16.6 1.0 HB2 C:ASP282 3.5 19.1 1.0 HA C:LEU285 3.5 16.4 1.0 H C:VAL287 3.7 12.4 1.0 HA C:ASP282 3.7 16.3 1.0 CA C:ASP282 4.1 16.3 1.0 CA C:SER288 4.2 12.1 1.0 CA C:LEU285 4.2 16.4 1.0 N C:LEU285 4.2 16.4 1.0 CB C:ASP282 4.2 19.1 1.0 C C:SER283 4.2 16.8 1.0 N C:SER288 4.3 11.9 1.0 N C:VAL287 4.3 12.4 1.0 N C:SER284 4.3 17.0 1.0 HB C:VAL287 4.3 14.1 1.0 C C:LEU285 4.4 14.6 1.0 O C:SER283 4.4 16.9 1.0 O C:LEU285 4.4 16.1 1.0 CA C:VAL287 4.5 12.7 1.0 HA C:SER283 4.5 17.8 1.0 N C:SER283 4.5 18.2 1.0 CA C:SER284 4.5 17.8 1.0 O C:SER288 4.6 14.7 1.0 C C:SER288 4.6 12.2 1.0 H C:SER284 4.6 17.0 1.0 HB3 C:ASP282 4.7 19.1 1.0 CA C:SER283 4.7 17.8 1.0 CB C:VAL287 4.9 14.1 1.0 HD12 C:LEU285 5.0 20.2 1.0 H C:LEU285 5.0 16.4 1.0 N C:ARG286 5.0 15.6 1.0

Sodium binding site 6 out of 6 in the Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Pet Hydrolase PET6 From Halophilic Organsim Vibrio Gazogenes within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:28.9 occ:1.00 O C:ARG61 2.1 29.9 1.0 O C:ALA63 2.4 22.2 1.0 O C:PHE66 2.4 12.1 1.0 O C:HOH556 2.4 22.4 1.0 O C:HOH531 3.1 17.0 1.0 C C:ARG61 3.2 25.5 1.0 C C:PHE66 3.5 10.0 1.0 C C:ALA63 3.5 20.3 1.0 HA2 C:GLY67 3.5 10.8 1.0 H C:PHE66 3.6 11.3 1.0 HA C:ARG61 3.7 25.7 0.7 HA C:ARG61 3.7 25.7 0.3 N C:ALA63 3.8 22.8 1.0 C C:LEU62 3.9 23.9 1.0 H C:ALA63 3.9 22.8 1.0 CA C:ARG61 4.0 24.7 0.7 HA C:LEU62 4.0 26.6 1.0 HB3 C:ARG61 4.0 28.6 0.7 CA C:ARG61 4.0 25.7 0.3 H C:GLY65 4.0 15.1 1.0 OD1 C:ASN117 4.0 13.8 1.0 HB3 C:ALA63 4.1 21.3 1.0 N C:LEU62 4.1 25.0 1.0 CA C:ALA63 4.2 22.0 1.0 N C:PHE66 4.2 11.3 1.0 CA C:LEU62 4.2 26.6 1.0 O C:LEU62 4.3 27.7 1.0 CA C:GLY67 4.3 10.7 1.0 N C:GLY67 4.3 10.3 1.0 HB3 C:ARG61 4.3 28.6 0.3 H C:GLY68 4.4 10.6 1.0 HG2 C:ARG61 4.5 30.4 0.3 CA C:PHE66 4.5 10.6 1.0 HA C:ARG64 4.5 20.5 0.8 N C:GLY65 4.6 15.1 1.0 CB C:ARG61 4.6 27.6 0.7 HA C:ARG64 4.6 20.5 0.2 N C:ARG64 4.6 20.8 1.0 CB C:ALA63 4.7 21.3 1.0 CB C:ARG61 4.7 28.6 0.3 N C:GLY68 4.8 10.6 1.0 C C:GLY67 4.8 11.9 1.0 O C:HOH428 4.9 27.0 1.0 H C:LEU62 4.9 25.0 1.0 CA C:ARG64 5.0 21.2 0.8 HA C:PHE66 5.0 10.6 1.0 CA C:ARG64 5.0 20.5 0.2 C C:ARG64 5.0 17.9 1.0

S.Weigert, P.Perez-Garcia, F.J.Gisdon, A.Gagsteiger, K.Schweinshaut, G.M.Ullmann, J.Chow, W.R.Streit, B.Hocker. Investigation of the Halophilic Pet Hydrolase PET6 From Vibrio Gazogenes. Protein Sci. V. 31 E4500 2022.
ISSN: ESSN 1469-896X
PubMed: 36336469
DOI: 10.1002/PRO.4500