Zinc in PDB 8osw: Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1)

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1), PDB code: 8osw was solved by J.Loch, P.Worsztynowicz, J.Sliwiak, B.Imiolczyk, M.Grzechowiak, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.20 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.762, 85.889, 82.723, 90, 108.72, 90
R / Rfree (%)	13.4 / 16.3

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1) 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 Reaiv (R4MC-1) (pdb code 8osw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1), PDB code: 8osw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1)


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 Reaiv (R4MC-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.7 occ:0.50 O A:HOH501 1.9 13.4 0.5 SG A:CYS134 2.3 12.6 0.5 SG A:CYS188 2.3 13.6 0.5 O A:HOH503 2.3 39.6 1.0 NZ A:LYS137 2.4 21.8 1.0 OD2 A:ASP186 3.2 14.2 0.5 CE A:LYS137 3.2 20.6 1.0 CB A:CYS134 3.3 12.1 0.5 CB A:CYS188 3.3 13.1 0.5 CB A:CYS134 3.4 12.8 0.5 CB A:CYS188 3.5 13.1 0.5 CE A:LYS50 3.8 12.9 1.0 OD2 A:ASP186 3.8 13.8 0.5 SG A:CYS188 3.8 13.9 0.5 CG A:ASP186 3.9 13.2 0.5 OD1 A:ASP186 4.1 14.6 0.5 NZ A:LYS50 4.2 13.2 1.0 SG A:CYS134 4.2 13.3 0.5 OG A:SER47 4.3 15.0 0.5 CG A:ASP186 4.3 11.5 0.5 O A:HOH539 4.3 20.0 1.0 NE2 A:HIS138 4.4 13.0 1.0 N A:CYS188 4.4 12.6 0.5 N A:CYS188 4.4 12.9 0.5 O A:HOH804 4.5 50.1 1.0 CA A:CYS188 4.5 13.1 0.5 O A:HOH520 4.5 39.5 1.0 CA A:CYS188 4.6 13.2 0.5 CD A:LYS137 4.6 20.6 1.0 CA A:CYS134 4.7 11.8 0.5 CA A:CYS134 4.7 12.4 0.5 O A:HOH516 4.8 27.0 1.0 CB A:ASP186 4.8 12.6 0.5 OD1 A:ASP186 4.8 11.3 0.5 CD2 A:HIS138 4.9 13.7 1.0 CD1 A:ILE190 5.0 17.4 1.0 CB A:ASP186 5.0 13.4 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (R4MC-1)


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 Reaiv (R4MC-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.7 occ:0.50 O B:HOH502 1.9 31.5 0.7 NZ B:LYS137 2.2 14.1 0.6 SG B:CYS134 2.3 11.7 0.5 O B:HOH506 2.3 38.2 1.0 SG B:CYS188 2.3 11.8 0.5 NZ B:LYS137 3.0 18.8 0.4 CE B:LYS137 3.0 13.9 0.6 OD2 B:ASP186 3.3 15.0 0.5 CB B:CYS134 3.3 11.6 0.5 CB B:CYS134 3.4 12.7 0.5 CB B:CYS188 3.4 10.9 0.5 CB B:CYS188 3.4 14.0 0.5 SG B:CYS188 3.7 14.7 0.5 CE B:LYS50 3.8 13.5 1.0 OD2 B:ASP186 3.8 16.2 0.5 CG B:ASP186 3.9 14.0 0.5 OD1 B:ASP186 4.1 14.2 0.5 SG B:CYS134 4.2 14.4 0.5 CE B:LYS137 4.2 17.8 0.4 NZ B:LYS50 4.2 13.5 1.0 OG B:SER47 4.3 17.9 0.5 CG B:ASP186 4.3 13.6 0.5 O B:HOH540 4.3 18.5 1.0 CD B:LYS137 4.4 12.4 0.6 NE2 B:HIS138 4.4 13.3 1.0 N B:CYS188 4.4 12.9 0.5 N B:CYS188 4.4 12.1 0.5 CA B:CYS188 4.5 11.9 0.5 O B:HOH504 4.5 35.8 1.0 CA B:CYS188 4.5 13.5 0.5 CA B:CYS134 4.6 11.0 0.5 CA B:CYS134 4.7 11.8 0.5 O B:HOH800 4.7 43.5 1.0 OD1 B:ASP186 4.8 13.1 0.5 O B:HOH512 4.8 25.2 1.0 CB B:ASP186 4.8 13.0 0.5 CD B:LYS137 4.9 16.6 0.4 CD2 B:HIS138 4.9 13.1 1.0 CD1 B:ILE190 5.0 14.9 1.0

J.I.Loch, P.Worsztynowicz, J.Sliwiak, M.Grzechowiak, B.Imiolczyk, K.Pokrywka, M.Chwastyk, M.Gilski, M.Jaskolski. Rhizobium Etli Has Two L-Asparaginases with Low Sequence Identity But Similar Structure and Catalytic Center. Acta Crystallogr D Struct V. 79 775 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37494066
DOI: 10.1107/S2059798323005648