Chlorine in PDB 8d5r: Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine

All present enzymatic activity of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine:
4.1.1.116;

The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine, PDB code: 8d5r was solved by R.S.Phillips, K.N.Nguyen Hoang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.34 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.53, 50.2, 140.28, 90, 116, 90
R / Rfree (%)	16.5 / 19

The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine (pdb code 8d5r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine, PDB code: 8d5r:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:27.3 occ:0.56 O A:HOH974 2.9 34.5 1.0 CB A:PRO208 3.7 30.6 1.0 CG A:PRO208 3.8 29.4 1.0 CD A:PRO208 4.0 32.1 1.0 O A:HOH834 4.2 47.5 1.0 CA A:PRO208 4.6 33.3 1.0 NH2 A:ARG158 4.7 35.6 1.0 N A:PRO208 4.7 28.3 1.0 O A:ALA206 4.7 38.5 1.0

Chlorine binding site 2 out of 2 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:33.1 occ:1.00 O B:HOH843 3.2 32.1 1.0 O B:HOH779 3.3 36.5 1.0 N B:THR75 3.3 20.7 1.0 O B:HOH876 3.6 42.1 1.0 O B:THR75 3.7 22.0 1.0 CA B:LYS74 4.0 23.3 1.0 SG B:CYS97 4.0 23.7 1.0 CA B:ILE96 4.0 21.4 1.0 CG B:LYS74 4.1 31.1 1.0 C B:LYS74 4.1 25.2 1.0 CA B:THR75 4.2 21.5 1.0 CB B:THR75 4.2 23.3 1.0 O B:GLY95 4.2 25.6 1.0 N B:CYS97 4.3 19.3 1.0 OE1 B:GLN64 4.3 33.2 1.0 CB B:ILE96 4.4 19.6 1.0 C B:THR75 4.4 19.9 1.0 CG2 B:ILE96 4.4 21.6 1.0 C B:ILE96 4.5 22.5 1.0 CB B:LYS74 4.6 28.1 1.0 OG1 B:THR75 4.6 24.5 1.0 O B:THR73 4.6 31.5 1.0 CB B:CYS97 4.8 19.2 1.0

R.S.Phillips, K.N.Nguyen Hoang. The Y430F Mutant of Salmonella D-Ornithine/D-Lysine Decarboxylase Has Altered Stereospecificity and A Putrescine Allosteric Activation Site. Arch.Biochem.Biophys. V. 731 09429 2022.
ISSN: ESSN 1096-0384
PubMed: 36265649
DOI: 10.1016/J.ABB.2022.109429