Sodium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with Putrescine, PDB code: 8d4i:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na509 b:19.7 occ:1.00 O A:HOH1058 2.3 54.7 1.0 O A:VAL210 2.4 19.1 1.0 O A:MET207 2.5 21.6 1.0 O A:ILE204 2.5 17.8 1.0 O A:HOH1026 2.9 24.4 1.0 O A:LEU205 3.0 27.2 1.0 HA A:LEU205 3.1 24.0 1.0 C A:LEU205 3.5 21.4 1.0 H A:MET207 3.5 22.8 1.0 C A:MET207 3.6 20.7 1.0 C A:VAL210 3.6 14.9 1.0 C A:ILE204 3.6 19.4 1.0 CA A:LEU205 3.7 20.0 1.0 HB2 A:MET207 3.7 23.7 1.0 H A:VAL210 3.7 19.3 1.0 HA A:HIS211 3.8 18.8 1.0 N A:MET207 3.8 18.9 1.0 HG22 A:ILE204 4.0 21.4 1.0 N A:LEU205 4.1 19.9 1.0 CA A:MET207 4.1 17.6 1.0 HB A:VAL210 4.1 17.9 1.0 HG23 A:ILE204 4.2 21.4 1.0 O A:HOH1025 4.3 36.0 1.0 O A:HOH934 4.3 42.8 1.0 N A:ALA206 4.4 20.5 1.0 N A:VAL210 4.4 16.1 1.0 CB A:MET207 4.4 19.8 1.0 CA A:VAL210 4.5 14.5 1.0 H A:LEU212 4.5 18.8 1.0 N A:HIS211 4.5 15.4 1.0 CG2 A:ILE204 4.5 17.8 1.0 C A:ALA206 4.6 22.5 1.0 CA A:HIS211 4.6 15.6 1.0 HA A:PRO208 4.6 23.4 1.0 N A:PRO208 4.7 19.2 1.0 HD23 A:LEU205 4.8 34.7 1.0 HB3 A:MET207 4.8 23.7 1.0 CB A:VAL210 4.8 14.9 1.0 CA A:ILE204 4.9 17.4 1.0 O A:HOH986 4.9 37.9 1.0 HA A:ILE204 4.9 20.9 1.0 H A:ALA206 4.9 24.7 1.0 C A:PRO208 4.9 20.9 1.0 H A:LEU205 5.0 23.9 1.0 CA A:PRO208 5.0 19.5 1.0 CA A:ALA206 5.0 22.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na505 b:18.4 occ:1.00 O C:VAL210 2.4 19.8 1.0 O C:HOH1069 2.4 54.8 1.0 O C:MET207 2.5 20.1 1.0 O C:ILE204 2.6 19.1 1.0 O C:HOH1058 2.9 25.0 1.0 O C:LEU205 3.0 30.0 1.0 HA C:LEU205 3.1 29.1 1.0 C C:LEU205 3.4 23.9 1.0 H C:MET207 3.5 22.3 1.0 C C:VAL210 3.6 16.9 1.0 CA C:LEU205 3.6 24.2 1.0 C C:MET207 3.6 21.3 1.0 HB2 C:MET207 3.6 22.7 1.0 C C:ILE204 3.7 17.8 1.0 HA C:HIS211 3.8 19.8 1.0 N C:MET207 3.8 18.6 1.0 H C:VAL210 3.8 19.0 1.0 HG22 C:ILE204 4.0 19.5 1.0 N C:LEU205 4.1 21.3 1.0 CA C:MET207 4.2 17.6 1.0 HB C:VAL210 4.2 19.2 1.0 HG23 C:ILE204 4.2 19.5 1.0 O C:HOH998 4.2 34.3 1.0 O C:HOH1043 4.3 45.0 1.0 N C:ALA206 4.3 23.4 1.0 O C:HOH1149 4.3 39.7 1.0 CB C:MET207 4.4 18.9 1.0 N C:VAL210 4.5 15.8 1.0 H C:LEU212 4.5 17.7 1.0 C C:ALA206 4.5 26.8 1.0 CA C:VAL210 4.5 15.2 1.0 N C:HIS211 4.5 14.9 1.0 CA C:HIS211 4.6 16.5 1.0 CG2 C:ILE204 4.6 16.2 1.0 HD23 C:LEU205 4.6 38.7 1.0 HA C:PRO208 4.7 23.7 1.0 N C:PRO208 4.8 18.2 1.0 HB3 C:MET207 4.8 22.7 1.0 H C:ALA206 4.8 28.1 1.0 CB C:VAL210 4.9 15.9 1.0 CA C:ALA206 4.9 30.2 1.0 CA C:ILE204 4.9 17.4 1.0 HA C:ILE204 5.0 20.9 1.0 H C:LEU205 5.0 25.6 1.0 CB C:LEU205 5.0 27.8 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