Zinc in PDB 8ruf: Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant, PDB code: 8ruf 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)	48.57 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.715, 91.26, 114.197, 90, 96.95, 90
R / Rfree (%)	15.8 / 18.4

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant (pdb code 8ruf). 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 D187A Mutant, PDB code: 8ruf:
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 D187A 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 D187A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:21.5 occ:0.50 O A:HOH502 2.2 30.4 0.5 NZ A:LYS138 2.2 22.4 1.0 SG A:CYS189 2.3 27.3 1.0 SG A:CYS135 2.3 22.0 1.0 CB A:CYS189 3.0 27.9 1.0 CE A:LYS138 3.1 19.7 1.0 O1 A:SO4401 3.1 27.4 1.0 CB A:CYS135 3.3 18.4 1.0 O A:HOH532 4.0 22.8 1.0 O3 A:SO4401 4.1 39.7 1.0 CE A:LYS51 4.1 20.0 1.0 S A:SO4401 4.1 35.6 1.0 O A:HOH681 4.2 20.0 1.0 O A:HOH528 4.2 34.2 1.0 CA A:CYS189 4.2 23.5 1.0 N A:CYS189 4.3 21.8 1.0 CB A:ALA187 4.3 23.9 1.0 O A:HOH564 4.4 23.5 1.0 NZ A:LYS51 4.5 21.1 1.0 CD A:LYS138 4.5 19.4 1.0 CA A:CYS135 4.7 18.2 1.0 O2 A:SO4401 4.8 42.6 1.0 NE2 A:HIS139 4.9 17.0 1.0 CD1 A:LEU191 4.9 20.5 1.0 OG A:SER48 4.9 25.7 1.0 O A:HOH508 5.0 28.3 1.0 C A:CYS189 5.0 26.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A 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 D187A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:20.6 occ:0.50 O B:HOH507 2.0 23.4 0.5 NZ B:LYS138 2.2 19.5 1.0 SG B:CYS189 2.2 25.5 1.0 SG B:CYS135 2.3 21.4 1.0 CB B:CYS189 2.9 26.4 1.0 CE B:LYS138 3.1 18.8 1.0 O2 B:SO4401 3.1 27.4 1.0 CB B:CYS135 3.3 14.8 1.0 O4 B:SO4401 4.0 29.9 1.0 CE B:LYS51 4.0 17.5 1.0 O B:HOH531 4.1 19.4 1.0 O B:HOH723 4.1 17.7 1.0 S B:SO4401 4.1 30.6 1.0 O B:HOH519 4.2 30.9 1.0 CA B:CYS189 4.2 23.6 1.0 CB B:ALA187 4.3 17.8 1.0 N B:CYS189 4.3 22.6 1.0 NZ B:LYS51 4.3 17.3 1.0 O B:HOH550 4.4 21.3 1.0 CD B:LYS138 4.5 17.9 1.0 CA B:CYS135 4.7 15.6 1.0 OG B:SER48 4.9 22.0 1.0 O B:HOH503 4.9 27.3 1.0 CD1 B:LEU191 5.0 20.3 1.0 C B:CYS189 5.0 25.4 1.0 O1 B:SO4401 5.0 34.9 1.0 NE2 B:HIS139 5.0 17.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A 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 D187A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:19.9 occ:0.50 O C:HOH501 1.9 25.0 0.5 NZ C:LYS138 2.2 21.8 1.0 SG C:CYS189 2.3 25.3 1.0 SG C:CYS135 2.3 23.8 1.0 CB C:CYS189 2.9 24.4 1.0 O3 C:SO4401 3.0 28.8 1.0 CE C:LYS138 3.1 21.5 1.0 CB C:CYS135 3.3 17.6 1.0 O1 C:SO4401 4.0 35.4 1.0 CE C:LYS51 4.0 17.6 1.0 O C:HOH529 4.0 23.3 1.0 S C:SO4401 4.0 35.7 1.0 O C:HOH709 4.1 17.5 1.0 CA C:CYS189 4.2 26.9 1.0 CB C:ALA187 4.2 21.7 1.0 O C:HOH531 4.2 35.8 1.0 N C:CYS189 4.2 22.1 1.0 NZ C:LYS51 4.4 18.6 1.0 O C:HOH537 4.4 20.2 1.0 CD C:LYS138 4.5 17.7 1.0 CA C:CYS135 4.6 15.4 1.0 O4 C:SO4401 4.8 40.1 1.0 C C:CYS189 4.9 28.7 1.0 NE2 C:HIS139 5.0 18.5 1.0 OG C:SER48 5.0 26.1 1.0 CD1 C:LEU191 5.0 19.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A 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 D187A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn408 b:20.1 occ:0.50 O D:HOH503 2.1 26.4 0.5 NZ D:LYS138 2.2 19.2 1.0 SG D:CYS189 2.3 25.7 1.0 SG D:CYS135 2.3 22.7 1.0 CB D:CYS189 3.0 28.2 1.0 CE D:LYS138 3.0 20.4 1.0 O3 D:SO4401 3.1 29.3 1.0 CB D:CYS135 3.3 16.7 1.0 CE D:LYS51 3.9 19.8 1.0 O1 D:SO4401 4.0 28.1 1.0 O D:HOH533 4.0 21.4 1.0 S D:SO4401 4.1 30.9 1.0 O D:HOH527 4.1 30.5 1.0 O D:HOH686 4.2 17.4 1.0 CA D:CYS189 4.2 22.0 1.0 CB D:ALA187 4.3 19.7 1.0 NZ D:LYS51 4.3 19.1 1.0 N D:CYS189 4.3 21.5 1.0 O D:HOH554 4.3 21.2 1.0 CD D:LYS138 4.5 17.2 1.0 CA D:CYS135 4.6 16.9 1.0 OG D:SER48 4.8 26.4 1.0 O4 D:SO4401 4.9 37.3 1.0 O D:HOH509 4.9 25.4 1.0 NE2 D:HIS139 4.9 16.9 1.0 CD1 D:LEU191 5.0 17.9 1.0 C D:CYS189 5.0 25.3 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