Chlorine in PDB 8d88: Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine

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

The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine, PDB code: 8d88 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)	41.28 / 1.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.24, 50.49, 139.32, 90, 117.26, 90
R / Rfree (%)	17.5 / 19.5

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

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine (pdb code 8d88). 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- Lysine, PDB code: 8d88:
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- Lysine


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- Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl509 b:35.0 occ:1.00 O A:HOH754 3.1 38.8 1.0 N A:THR75 3.2 27.6 1.0 O A:HOH719 3.6 36.8 1.0 O A:HOH973 3.7 51.3 1.0 O A:THR75 3.8 27.4 1.0 CA A:LYS74 3.9 26.7 1.0 SG A:CYS97 4.0 27.7 1.0 CG A:LYS74 4.0 36.8 1.0 CA A:ILE96 4.0 26.0 1.0 C A:LYS74 4.1 27.0 1.0 CA A:THR75 4.1 25.4 1.0 O A:GLY95 4.1 29.4 1.0 CB A:THR75 4.2 25.5 1.0 N A:CYS97 4.3 24.1 1.0 C A:THR75 4.4 25.1 1.0 CG2 A:ILE96 4.4 27.3 1.0 CB A:ILE96 4.4 23.2 1.0 OE1 A:GLN64 4.5 43.4 1.0 C A:ILE96 4.5 29.2 1.0 O A:THR73 4.5 35.0 1.0 CB A:LYS74 4.6 30.5 1.0 OG1 A:THR75 4.6 29.1 1.0 CB A:CYS97 4.8 23.6 1.0

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


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- Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:32.5 occ:1.00 O B:HOH870 3.1 32.2 1.0 N B:THR75 3.2 22.7 1.0 O B:HOH810 3.6 31.0 1.0 O B:HOH902 3.7 44.1 1.0 O B:THR75 3.7 22.1 1.0 CA B:LYS74 3.9 25.0 1.0 CA B:ILE96 4.0 22.7 1.0 SG B:CYS97 4.0 25.3 1.0 CG B:LYS74 4.1 28.5 1.0 C B:LYS74 4.1 23.2 1.0 O B:GLY95 4.1 27.3 1.0 CA B:THR75 4.1 22.2 1.0 CB B:THR75 4.2 24.1 1.0 N B:CYS97 4.2 21.0 1.0 OE1 B:GLN64 4.3 34.8 1.0 CB B:ILE96 4.3 23.0 1.0 C B:THR75 4.4 24.3 1.0 CG2 B:ILE96 4.4 24.7 1.0 C B:ILE96 4.5 27.1 1.0 O B:THR73 4.5 32.4 1.0 CB B:LYS74 4.6 26.2 1.0 OG1 B:THR75 4.6 25.0 1.0 CB B:CYS97 4.8 19.1 1.0 C B:GLY95 5.0 25.6 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