Sodium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine, PDB code: 8d5r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na505 b:26.3 occ:1.00 O A:VAL210 2.3 25.3 1.0 O A:ILE204 2.3 28.8 1.0 O A:HOH642 2.4 57.4 1.0 O A:MET207 2.4 31.4 1.0 O A:HOH948 2.9 28.4 0.6 O A:LEU205 2.9 36.7 1.0 C A:LEU205 3.3 28.1 1.0 C A:ILE204 3.4 25.1 1.0 C A:MET207 3.5 31.4 1.0 C A:VAL210 3.5 23.0 1.0 CA A:LEU205 3.6 29.5 1.0 N A:MET207 3.6 27.2 1.0 CA A:MET207 4.0 25.8 1.0 N A:LEU205 4.0 29.6 1.0 N A:ALA206 4.2 28.6 1.0 N A:VAL210 4.2 23.7 1.0 CB A:MET207 4.2 25.8 1.0 O A:HOH890 4.3 30.7 0.7 OXT A:ACT503 4.3 58.1 1.0 CA A:VAL210 4.3 23.3 1.0 C A:ALA206 4.3 35.9 1.0 O A:HOH874 4.4 51.9 1.0 O A:ACT503 4.4 60.3 1.0 CG2 A:ILE204 4.5 26.3 1.0 N A:HIS211 4.5 21.7 1.0 CB A:VAL210 4.6 22.5 1.0 N A:PRO208 4.6 28.3 1.0 CA A:ILE204 4.7 25.3 1.0 CA A:HIS211 4.7 23.0 1.0 C A:ACT503 4.7 64.8 1.0 CA A:ALA206 4.8 38.0 1.0 C A:PRO208 4.9 29.3 1.0 CA A:PRO208 4.9 33.3 1.0 O A:HOH916 5.0 49.0 1.0 CB A:LEU205 5.0 31.3 1.0

Sodium binding site 2 out of 3 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na507 b:29.5 occ:1.00 O B:VAL210 2.3 30.3 1.0 O B:MET207 2.4 36.3 1.0 O B:HOH973 2.4 47.8 1.0 O B:ILE204 2.5 31.1 1.0 O B:LEU205 2.9 40.5 1.0 C B:LEU205 3.3 34.5 1.0 C B:MET207 3.5 35.2 1.0 C B:VAL210 3.5 28.0 1.0 C B:ILE204 3.6 30.2 1.0 CA B:LEU205 3.6 32.9 1.0 N B:MET207 3.7 32.7 1.0 CA B:MET207 4.0 33.5 1.0 N B:LEU205 4.1 31.4 1.0 O B:HOH913 4.1 36.6 1.0 CB B:MET207 4.2 34.4 1.0 N B:VAL210 4.2 32.7 1.0 N B:ALA206 4.2 34.9 1.0 CA B:VAL210 4.3 29.2 1.0 O B:HOH933 4.3 53.0 1.0 C B:ALA206 4.3 33.4 1.0 N B:HIS211 4.5 26.6 1.0 CB B:VAL210 4.5 27.6 1.0 N B:PRO208 4.6 34.5 1.0 CG2 B:ILE204 4.6 30.0 1.0 CA B:HIS211 4.7 26.4 1.0 CA B:ALA206 4.7 34.9 1.0 CA B:ILE204 4.8 28.2 1.0 C B:PRO208 4.9 32.9 1.0 CA B:PRO208 4.9 30.9 1.0

Sodium binding site 3 out of 3 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 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:Na508 b:40.2 occ:1.00 OE1 B:GLU322 2.4 40.4 1.0 O B:HOH747 2.5 42.4 1.0 O B:HOH978 2.5 73.4 1.0 OG1 B:THR46 2.5 20.4 1.0 O B:HOH906 2.5 35.9 1.0 CD B:GLU322 3.5 43.8 1.0 O B:HOH742 3.5 40.5 1.0 N B:THR46 3.7 24.5 1.0 CB B:THR46 3.7 18.7 1.0 CG2 B:THR46 4.0 22.4 1.0 CB B:GLU322 4.1 19.5 1.0 NZ A:LYS127 4.2 29.6 1.0 OD2 B:ASP348 4.2 19.8 1.0 OE2 B:GLU322 4.2 37.1 1.0 O B:HOH812 4.3 47.1 1.0 CA B:THR46 4.3 20.6 1.0 CG B:GLU322 4.4 23.2 1.0 O B:THR46 4.6 21.5 1.0 C B:PRO45 4.7 26.4 1.0 CA B:PRO45 4.8 33.4 1.0 O B:ALA41 4.8 32.9 1.0 C B:THR46 4.8 23.4 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