Cadmium in PDB 9g66: Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn

The structure of Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn, PDB code: 9g66 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)	45.66 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.964, 91.329, 106.061, 90, 90, 90
R / Rfree (%)	17.4 / 22.1

The binding sites of Cadmium atom in the Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn (pdb code 9g66). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn, PDB code: 9g66:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd418 b:25.4 occ:1.00 SG A:CYS135 2.5 20.1 1.0 NZ A:LYS138 2.5 17.7 1.0 SG A:CYS189 2.6 20.6 1.0 N A:ASN413 2.7 24.4 0.7 O A:HOH617 2.7 20.6 0.3 O A:ASN413 2.8 22.1 0.7 CE A:LYS138 3.3 20.7 1.0 CB A:CYS135 3.3 21.8 1.0 CB A:CYS189 3.4 21.2 1.0 C A:ASN413 3.5 21.4 0.7 CA A:ASN413 3.6 22.7 0.7 OD2 A:ASP187 3.6 24.9 1.0 CG A:ASP187 4.0 21.2 1.0 CE A:LYS51 4.1 21.4 1.0 CB A:ASN413 4.1 24.5 0.7 O A:HOH677 4.2 19.4 1.0 CB A:ASP187 4.3 21.9 1.0 N A:CYS189 4.4 19.5 1.0 O A:HOH553 4.4 21.4 1.0 NZ A:LYS51 4.4 25.2 1.0 CA A:CYS189 4.5 19.9 1.0 OXT A:ASN413 4.7 26.8 0.7 CD A:LYS138 4.7 20.5 1.0 OG A:SER48 4.7 24.1 0.7 CA A:CYS135 4.7 18.9 1.0 OD1 A:ASP187 4.8 25.9 1.0 NE2 A:HIS139 4.9 22.5 1.0 CD1 A:LEU191 5.0 20.4 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Wt Rhizobium Etli L-Asparaginase Reav in Complex with L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd410 b:25.2 occ:1.00 NZ B:LYS138 2.5 19.2 1.0 SG B:CYS189 2.5 20.4 1.0 SG B:CYS135 2.5 21.1 1.0 O B:HOH577 2.5 16.0 0.3 N B:ASN409 2.7 24.5 0.7 O B:ASN409 3.0 25.3 0.7 CE B:LYS138 3.2 18.8 1.0 CB B:CYS189 3.3 17.0 1.0 CB B:CYS135 3.3 21.2 1.0 C B:ASN409 3.4 24.1 0.7 CA B:ASN409 3.6 25.7 0.7 OD2 B:ASP187 3.8 26.1 1.0 CG B:ASP187 4.1 25.8 1.0 CE B:LYS51 4.1 21.9 1.0 OXT B:ASN409 4.2 24.4 0.7 O B:HOH662 4.2 18.8 1.0 CB B:ASP187 4.3 18.9 1.0 N B:CYS189 4.4 17.5 1.0 NZ B:LYS51 4.4 21.9 1.0 CA B:CYS189 4.4 19.5 1.0 O B:HOH566 4.4 19.3 1.0 CB B:ASN409 4.4 25.0 0.7 CD B:LYS138 4.6 19.6 1.0 OG B:SER48 4.6 24.1 1.0 CA B:CYS135 4.7 20.3 1.0 OD1 B:ASP187 4.8 24.6 1.0 NE2 B:HIS139 4.9 19.5 1.0

K.Pokrywka, M.Grzechowiak, J.Sliwiak, P.Worsztynowicz, J.I.Loch, M.Ruszkowski, M.Gilski, M.Jaskolski. Controlling Enzyme Activity By Mutagenesis and Metal Exchange to Obtain Crystal Structures of Stable Substrate Complexes of Class 3 L-Asparaginase. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 39754186
DOI: 10.1111/FEBS.17388