Sodium in PDB 8otu: The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii

The structure of The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii, PDB code: 8otu was solved by E.Costanzi, V.Applegate, S.H.J.Smits, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.31 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.133, 45.66, 84.187, 90, 97.83, 90
R / Rfree (%)	13.2 / 15

The structure of The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii (pdb code 8otu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii, PDB code: 8otu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:23.4 occ:1.00 HO2 A:EDO415 2.2 43.6 1.0 O A:VAL72 2.2 24.8 1.0 O A:SER70 2.3 24.3 1.0 O A:PHE75 2.3 19.3 1.0 O A:HOH675 2.4 32.9 1.0 O2 A:EDO415 2.4 36.3 1.0 O A:HOH585 2.7 31.6 1.0 H21 A:EDO415 3.1 50.4 1.0 C2 A:EDO415 3.2 42.0 1.0 H22 A:EDO415 3.4 50.4 1.0 C A:VAL72 3.4 26.3 1.0 H A:PHE75 3.4 25.3 1.0 C A:SER70 3.5 22.5 1.0 HG12 A:VAL72 3.5 28.6 1.0 HA2 A:GLY76 3.5 22.6 1.0 C A:PHE75 3.5 17.9 1.0 C A:LEU71 3.9 23.4 1.0 N A:VAL72 3.9 23.9 1.0 H A:GLY74 3.9 26.5 1.0 HG13 A:VAL72 3.9 28.6 1.0 O A:HOH718 4.0 43.0 1.0 OD1 A:ASN126 4.0 25.1 1.0 HA A:SER70 4.0 26.1 1.0 HA A:ARG73 4.0 33.3 1.0 O A:LEU71 4.1 29.1 1.0 N A:PHE75 4.1 21.1 1.0 H A:VAL72 4.1 28.7 1.0 CG1 A:VAL72 4.1 23.8 1.0 HA A:LEU71 4.2 33.6 1.0 CA A:VAL72 4.2 22.7 1.0 O A:HOH705 4.2 42.8 1.0 HB2 A:SER70 4.2 28.1 1.0 CA A:GLY76 4.3 18.8 1.0 CA A:SER70 4.3 21.8 1.0 N A:GLY76 4.4 18.2 1.0 N A:LEU71 4.4 23.1 1.0 CA A:LEU71 4.4 28.0 1.0 N A:GLY74 4.4 22.1 1.0 N A:ARG73 4.4 25.9 1.0 CA A:PHE75 4.5 19.7 1.0 H A:GLY77 4.6 22.4 1.0 CA A:ARG73 4.6 27.7 1.0 C1 A:EDO415 4.6 43.8 1.0 C A:ARG73 4.7 25.4 1.0 CB A:SER70 4.8 23.4 1.0 CB A:VAL72 4.8 26.5 1.0 C A:GLY76 4.9 20.2 1.0 N A:GLY77 4.9 18.7 1.0 HG11 A:VAL72 4.9 28.6 1.0 HA A:PHE75 4.9 23.6 1.0

Sodium binding site 2 out of 3 in the The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:27.7 occ:1.00 O B:VAL72 2.3 32.5 1.0 O B:PHE75 2.3 26.6 1.0 O B:SER70 2.3 32.8 1.0 O B:HOH652 2.4 32.6 1.0 O B:HOH683 2.4 41.9 1.0 O B:HOH560 2.6 37.7 1.0 HA2 B:GLY76 3.4 30.6 1.0 C B:VAL72 3.5 30.8 1.0 C B:SER70 3.5 31.7 1.0 C B:PHE75 3.5 25.9 1.0 HG12 B:VAL72 3.5 34.7 1.0 H B:PHE75 3.6 30.4 1.0 OD1 B:ASN126 3.9 32.2 1.0 N B:VAL72 3.9 29.1 1.0 C B:LEU71 4.0 37.8 1.0 HG13 B:VAL72 4.0 34.7 1.0 HA B:LEU71 4.0 45.6 1.0 HA B:ARG73 4.1 37.5 1.0 H B:VAL72 4.1 35.0 1.0 HA B:SER70 4.1 36.6 1.0 H B:GLY74 4.1 33.8 1.0 CA B:GLY76 4.2 25.5 1.0 CG1 B:VAL72 4.2 28.9 1.0 N B:PHE75 4.3 25.4 1.0 CA B:VAL72 4.3 29.0 1.0 N B:GLY76 4.3 24.1 1.0 O B:LEU71 4.3 35.1 1.0 CA B:LEU71 4.3 38.0 1.0 N B:LEU71 4.4 31.9 1.0 HB2 B:SER70 4.4 41.1 1.0 CA B:SER70 4.4 30.5 1.0 N B:ARG73 4.5 34.6 1.0 CA B:PHE75 4.5 23.8 1.0 N B:GLY74 4.6 28.2 1.0 CA B:ARG73 4.6 31.2 1.0 H B:GLY77 4.6 29.2 1.0 C B:GLY76 4.8 26.7 1.0 C B:ARG73 4.8 30.4 1.0 N B:GLY77 4.9 24.4 1.0 HA3 B:GLY76 4.9 30.6 1.0 HA B:ASN126 4.9 33.2 1.0 CB B:VAL72 4.9 30.2 1.0 CB B:SER70 4.9 34.3 1.0 HA B:PHE75 4.9 28.5 1.0 HG11 B:VAL72 5.0 34.7 1.0

Sodium binding site 3 out of 3 in the The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:24.1 occ:1.00 O B:GLU291 2.2 29.4 1.0 O B:ILE296 2.3 24.1 1.0 O B:ASP293 2.5 25.0 1.0 O B:HOH605 2.5 34.8 1.0 O B:HOH665 2.5 38.6 1.0 C B:GLU291 3.3 25.7 1.0 C B:ILE296 3.5 23.7 1.0 H B:ILE296 3.5 27.7 1.0 HA B:ARG294 3.5 34.0 1.0 C B:ASP293 3.5 28.0 1.0 HA B:GLU291 3.6 28.3 1.0 HB3 B:GLU291 3.8 30.6 1.0 HA B:SER297 3.9 27.5 1.0 CA B:GLU291 3.9 23.6 1.0 HB B:ILE296 4.0 26.5 1.0 N B:ILE296 4.1 23.1 1.0 CA B:ARG294 4.2 28.4 1.0 C B:ARG292 4.2 29.3 1.0 N B:ASP293 4.2 26.4 1.0 CA B:ILE296 4.2 23.0 1.0 N B:ARG294 4.3 29.3 1.0 C B:ARG294 4.3 26.0 1.0 N B:ARG292 4.4 24.4 1.0 O B:ARG294 4.4 27.9 1.0 HA B:ARG292 4.4 31.6 1.0 CB B:GLU291 4.4 25.5 1.0 H B:ASP293 4.4 31.7 1.0 N B:SER297 4.4 22.0 1.0 O B:ARG292 4.5 35.3 1.0 CA B:ASP293 4.5 27.7 1.0 CA B:ARG292 4.6 26.3 1.0 CB B:ILE296 4.6 22.1 1.0 HG22 B:ILE296 4.6 28.6 1.0 CA B:SER297 4.6 22.9 1.0 HB3 B:ASP293 4.8 31.8 1.0 N B:GLN295 4.9 25.8 1.0 HG2 B:GLU291 4.9 27.5 1.0

E.Costanzi, V.Applegate, S.H.J.Smits. The Crystal Structure of PET44, A Petase Enzyme From Alkalilimnicola Ehrlichii To Be Published.