Cadmium in PDB 9g67: Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn, PDB code: 9g67 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)	63.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.233, 91.687, 106.283, 90, 90, 90
R / Rfree (%)	17.5 / 21.6

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn (pdb code 9g67). 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 Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn, PDB code: 9g67:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant 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 Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd509 b:26.0 occ:0.70 SG A:CYS189 2.6 30.0 1.0 N A:ASN505 2.6 31.6 1.0 SG A:CYS135 2.6 34.3 1.0 O A:ASN505 2.6 28.8 1.0 NZ A:LYS51 2.7 36.0 1.0 OD2 A:ASP187 3.2 31.7 1.0 C A:ASN505 3.4 31.8 1.0 CB A:CYS189 3.4 27.0 1.0 CA A:ASN505 3.5 33.3 1.0 CE A:LYS51 3.5 39.0 1.0 CB A:CYS135 3.6 26.1 1.0 CG A:ASP187 3.8 30.6 1.0 OG A:SER48 4.1 34.2 1.0 CB A:ASN505 4.2 34.3 1.0 CB A:ASP187 4.2 27.4 1.0 N A:CYS189 4.4 29.1 1.0 O A:HOH745 4.4 26.6 1.0 OD1 A:ASP187 4.5 28.9 1.0 OXT A:ASN505 4.5 33.7 1.0 CA A:CYS189 4.5 29.8 1.0 O A:HOH606 4.6 37.4 1.0 O A:HOH736 4.7 29.6 1.0 CD A:LYS51 4.8 31.2 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav K138H Mutant 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 Rhizobium Etli L-Asparaginase Reav K138H Mutant in Complex with L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd411 b:27.2 occ:0.70 N B:ASN408 2.5 38.5 1.0 OXT B:ASN408 2.6 34.2 1.0 SG B:CYS189 2.6 31.1 1.0 SG B:CYS135 2.6 34.1 1.0 NZ B:LYS51 2.7 40.7 1.0 OD2 B:ASP187 3.2 29.7 1.0 C B:ASN408 3.3 37.1 1.0 CE B:LYS51 3.4 38.1 1.0 CA B:ASN408 3.4 39.7 1.0 CB B:CYS189 3.5 32.4 1.0 CB B:CYS135 3.6 31.2 1.0 CG B:ASP187 3.7 31.1 1.0 OG B:SER48 4.0 30.1 1.0 CB B:ASP187 4.2 27.1 1.0 CB B:ASN408 4.2 41.9 1.0 N B:CYS189 4.2 26.5 1.0 OD1 B:ASP187 4.3 28.2 1.0 O B:HOH509 4.4 38.9 1.0 O B:ASN408 4.4 38.3 1.0 CA B:CYS189 4.5 32.4 1.0 O B:HOH582 4.5 29.6 1.0 O B:HOH568 4.8 35.4 1.0 CD B:LYS51 4.8 31.7 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