Zinc in PDB 8rue: Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant, PDB code: 8rue was solved by K.Pokrywka, M.Grzechowiak, J.Sliwiak, P.Worsztynowicz, J.I.Loch, M.Ruszkowski, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.87 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.906, 91.472, 114.471, 90, 96.98, 90
R / Rfree (%)	14.1 / 17.6

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant (pdb code 8rue). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant, PDB code: 8rue:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:18.0 occ:1.00 NZ A:LYS138 2.1 16.9 1.0 O A:HOH555 2.1 22.9 1.0 SG A:CYS135 2.3 15.7 1.0 SG A:CYS189 2.3 19.1 1.0 CE A:LYS138 3.0 16.1 1.0 CB A:CYS135 3.3 14.7 1.0 CB A:CYS189 3.3 14.8 1.0 O A:HOH795 3.7 39.1 1.0 OD2 A:ASP187 3.8 28.2 1.0 O A:HOH668 4.1 17.6 1.0 CE A:LYS51 4.1 15.9 1.0 CG A:ASP187 4.2 24.8 1.0 O A:HOH635 4.3 22.9 1.0 CB A:ASP187 4.4 18.4 1.0 N A:CYS189 4.4 13.6 1.0 O A:HOH775 4.4 18.7 1.0 CD A:LYS138 4.5 14.9 1.0 NZ A:LYS51 4.5 17.2 1.0 CA A:CYS189 4.5 14.3 1.0 O A:HOH502 4.5 23.6 1.0 CA A:CYS135 4.6 13.8 1.0 CD1 A:LEU191 4.8 17.5 1.0 OD1 A:ASP187 4.9 25.1 1.0 O A:HOH557 4.9 39.6 1.0 OG A:SER48 5.0 15.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:19.1 occ:1.00 NZ B:LYS138 2.1 15.9 1.0 SG B:CYS135 2.3 16.5 1.0 SG B:CYS189 2.3 19.5 1.0 O B:HOH501 2.3 26.1 1.0 OD2 B:ASP187 2.5 20.5 0.3 CE B:LYS138 3.0 14.8 1.0 CB B:CYS135 3.3 14.2 1.0 CB B:CYS189 3.3 16.2 1.0 CG B:ASP187 3.4 19.8 0.3 OD1 B:ASP187 3.6 20.9 0.3 O B:HOH793 3.8 31.7 1.0 OD2 B:ASP187 3.9 26.8 0.7 O B:HOH691 4.0 17.9 1.0 CG B:ASP187 4.1 23.8 0.7 CE B:LYS51 4.2 15.9 1.0 CB B:ASP187 4.2 17.6 0.7 O B:HOH554 4.4 26.3 1.0 N B:CYS189 4.4 14.5 1.0 O B:HOH790 4.4 18.5 1.0 CD B:LYS138 4.4 13.8 1.0 CA B:CYS189 4.5 14.7 1.0 NZ B:LYS51 4.5 16.9 1.0 CA B:CYS135 4.6 14.2 1.0 O B:HOH502 4.7 23.0 1.0 CB B:ASP187 4.8 18.0 0.3 CD1 B:LEU191 4.8 18.8 1.0 OD1 B:ASP187 4.8 24.5 0.7 O B:HOH504 4.8 32.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:19.0 occ:1.00 NZ C:LYS138 2.1 16.4 1.0 O C:HOH524 2.2 29.4 1.0 SG C:CYS135 2.3 16.1 1.0 SG C:CYS189 2.3 19.3 1.0 CE C:LYS138 3.1 15.8 1.0 CB C:CYS135 3.2 15.3 1.0 CB C:CYS189 3.3 16.6 1.0 O C:HOH794 3.7 37.0 1.0 OD2 C:ASP187 4.0 30.4 1.0 O C:HOH681 4.0 17.2 1.0 CG C:ASP187 4.1 26.0 1.0 CE C:LYS51 4.2 16.9 1.0 CB C:ASP187 4.2 19.1 1.0 O C:HOH775 4.4 20.3 1.0 N C:CYS189 4.4 14.8 1.0 O C:HOH556 4.4 26.3 1.0 CD C:LYS138 4.5 14.8 1.0 CA C:CYS189 4.5 15.2 1.0 NZ C:LYS51 4.5 17.3 1.0 CA C:CYS135 4.6 14.1 1.0 OD1 C:ASP187 4.7 26.6 1.0 O C:HOH501 4.7 24.6 1.0 O C:HOH505 4.8 50.1 1.0 CD1 C:LEU191 4.9 17.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rhizobium Etli L-Asparaginase Reav H139A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:19.4 occ:1.00 NZ D:LYS138 2.1 16.9 1.0 O D:HOH554 2.1 30.3 1.0 SG D:CYS135 2.3 16.9 1.0 SG D:CYS189 2.3 20.5 1.0 CE D:LYS138 3.0 16.8 1.0 CB D:CYS135 3.2 14.7 1.0 CB D:CYS189 3.3 17.4 1.0 O D:HOH785 3.8 34.6 1.0 OD2 D:ASP187 4.0 32.5 1.0 O D:HOH690 4.0 17.4 1.0 CG D:ASP187 4.1 28.0 1.0 CE D:LYS51 4.2 16.6 1.0 CB D:ASP187 4.2 20.1 1.0 O D:HOH549 4.4 24.9 1.0 CD D:LYS138 4.4 16.0 1.0 O D:HOH779 4.4 24.1 1.0 N D:CYS189 4.4 15.6 1.0 CA D:CYS189 4.5 17.0 1.0 NZ D:LYS51 4.6 18.0 1.0 CA D:CYS135 4.6 14.7 1.0 O D:HOH505 4.6 33.5 1.0 O D:HOH502 4.7 22.4 1.0 OD1 D:ASP187 4.7 28.9 1.0 CD1 D:LEU191 4.8 19.1 1.0

K.Pokrywka, M.Grzechowiak, J.Sliwiak, P.Worsztynowicz, J.I.Loch, M.Ruszkowski, M.Gilski, M.Jaskolski. Probing the Active Site of Class 3 L-Asparaginase By Mutagenesis. I. Tinkering with the Zinc Coordination Site of Reav Front Chem 2024.
ISSN: ESSN 2296-2646
DOI: 10.3389/FCHEM.2024.1381032