Chlorine in PDB 8d4i: Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with Putrescine

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

The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with Putrescine, PDB code: 8d4i 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)	41.36 / 1.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.88, 50.44, 139.18, 90, 116.93, 90
R / Rfree (%)	14.6 / 17.1

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

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with Putrescine (pdb code 8d4i). 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 Putrescine, PDB code: 8d4i:
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 Putrescine


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 Putrescine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl510 b:27.3 occ:1.00 H A:THR75 2.4 23.3 1.0 HA A:LYS74 3.1 22.0 1.0 HA A:ILE96 3.1 21.8 1.0 N A:THR75 3.2 19.4 1.0 HG3 A:LYS74 3.3 37.9 1.0 HB A:THR75 3.5 23.3 1.0 HG22 A:ILE96 3.6 20.7 1.0 O A:HOH722 3.7 31.4 1.0 O A:THR75 3.8 19.4 1.0 H A:CYS97 3.9 21.1 1.0 CA A:LYS74 3.9 18.3 1.0 HG2 A:LYS74 4.0 37.9 1.0 CG A:LYS74 4.0 31.5 1.0 CA A:ILE96 4.0 18.2 1.0 HB A:ILE96 4.0 19.1 1.0 SG A:CYS97 4.1 20.6 1.0 HE21 A:GLN64 4.1 39.5 1.0 HG1 A:THR75 4.1 26.0 1.0 C A:LYS74 4.1 19.3 1.0 O A:GLY95 4.1 23.8 1.0 CA A:THR75 4.1 17.7 1.0 HE22 A:GLN64 4.1 39.5 1.0 CB A:THR75 4.1 19.4 1.0 N A:CYS97 4.3 17.5 1.0 C A:THR75 4.4 16.4 1.0 CB A:ILE96 4.4 15.9 1.0 CG2 A:ILE96 4.4 17.2 1.0 NE2 A:GLN64 4.4 32.9 1.0 OG1 A:THR75 4.5 21.6 1.0 O A:THR73 4.6 25.6 1.0 CB A:LYS74 4.6 20.9 1.0 HB2 A:CYS97 4.6 21.6 1.0 C A:ILE96 4.6 21.6 1.0 HG A:CYS97 4.7 24.8 1.0 HE3 A:LYS74 4.8 53.3 1.0 CB A:CYS97 4.9 17.9 1.0 HG21 A:ILE96 4.9 20.7 1.0 HA A:THR75 5.0 21.2 1.0

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


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 Putrescine within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl506 b:24.5 occ:1.00 H C:THR75 2.4 17.7 1.0 HA C:LYS74 3.1 19.4 1.0 HA C:ILE96 3.1 16.9 1.0 O C:HOH898 3.2 23.8 1.0 N C:THR75 3.3 14.7 1.0 HG3 C:LYS74 3.3 27.4 1.0 HG22 C:ILE96 3.5 19.3 1.0 O C:HOH859 3.6 28.1 1.0 HB C:THR75 3.6 18.5 1.0 O C:HOH909 3.7 32.0 1.0 O C:THR75 3.8 15.2 1.0 H C:CYS97 3.9 15.5 1.0 HG C:CYS97 3.9 20.9 1.0 CA C:LYS74 3.9 16.1 1.0 HB C:ILE96 4.0 17.1 1.0 CA C:ILE96 4.0 14.0 1.0 SG C:CYS97 4.0 17.4 1.0 CG C:LYS74 4.1 22.8 1.0 C C:LYS74 4.1 14.2 1.0 HG2 C:LYS74 4.1 27.4 1.0 O C:GLY95 4.1 19.6 1.0 HG1 C:THR75 4.2 20.3 1.0 CA C:THR75 4.2 14.2 1.0 CB C:THR75 4.3 15.4 1.0 OE1 C:GLN64 4.3 23.1 1.0 N C:CYS97 4.3 12.9 1.0 CG2 C:ILE96 4.3 16.1 1.0 CB C:ILE96 4.4 14.2 1.0 C C:THR75 4.4 13.4 1.0 HB2 C:CYS97 4.5 15.5 1.0 O C:THR73 4.5 22.3 1.0 C C:ILE96 4.5 14.9 1.0 CB C:LYS74 4.6 17.9 1.0 OG1 C:THR75 4.7 16.9 1.0 CB C:CYS97 4.8 12.9 1.0 HG21 C:ILE96 4.9 19.3 1.0 HG23 C:ILE96 4.9 19.3 1.0 HE3 C:LYS74 4.9 29.8 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