Sodium in PDB 8d5d: Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Arginine

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

The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Arginine, PDB code: 8d5d 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)	48.86 / 1.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.77, 49.54, 139.56, 90, 115.93, 90
R / Rfree (%)	16.1 / 19.3

The binding sites of Sodium atom in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Arginine (pdb code 8d5d). 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 D- Arginine, PDB code: 8d5d:
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 D- Arginine


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- Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:29.1 occ:1.00 O A:VAL210 2.4 30.9 1.0 O A:ILE204 2.4 31.8 1.0 O A:MET207 2.4 37.4 1.0 O A:LEU205 2.8 38.8 1.0 HA A:LEU205 3.0 42.4 1.0 C A:LEU205 3.3 37.6 1.0 H A:MET207 3.4 39.9 1.0 C A:ILE204 3.5 28.4 1.0 C A:MET207 3.5 36.5 1.0 O A:HOH864 3.6 39.6 1.0 CA A:LEU205 3.6 35.3 1.0 C A:VAL210 3.6 26.2 1.0 HB2 A:MET207 3.6 36.0 1.0 H A:VAL210 3.6 35.0 1.0 N A:MET207 3.7 33.3 1.0 HA A:HIS211 3.9 29.6 1.0 HG22 A:ILE204 4.0 35.0 1.0 N A:LEU205 4.0 32.1 1.0 CA A:MET207 4.0 31.7 1.0 O A:HOH883 4.0 54.2 1.0 HB A:VAL210 4.1 28.8 1.0 HG23 A:ILE204 4.1 35.0 1.0 N A:ALA206 4.2 33.0 1.0 O A:HOH902 4.2 46.0 1.0 CB A:MET207 4.3 30.0 1.0 N A:VAL210 4.3 29.2 1.0 C A:ALA206 4.4 39.6 1.0 CA A:VAL210 4.5 25.5 1.0 CG2 A:ILE204 4.5 29.1 1.0 N A:HIS211 4.6 27.3 1.0 HA A:PRO208 4.6 42.7 1.0 H A:LEU212 4.6 32.8 1.0 N A:PRO208 4.6 34.6 1.0 CA A:HIS211 4.7 24.6 1.0 HB3 A:MET207 4.7 36.0 1.0 HD22 A:LEU205 4.7 45.6 1.0 H A:ALA206 4.7 39.6 1.0 CA A:ILE204 4.7 29.2 1.0 HA A:ILE204 4.7 35.0 1.0 CA A:ALA206 4.8 40.1 1.0 CB A:VAL210 4.8 24.0 1.0 C A:PRO208 4.8 36.2 1.0 H A:LEU205 4.8 38.6 1.0 O A:PRO208 4.9 35.4 1.0 CA A:PRO208 4.9 35.6 1.0 HA A:ALA206 4.9 48.1 1.0 CB A:LEU205 4.9 38.4 1.0 HA A:MET207 5.0 38.0 1.0

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


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- Arginine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:31.6 occ:1.00 O B:HOH933 2.0 40.3 1.0 O B:VAL210 2.3 32.1 1.0 O B:MET207 2.4 39.6 1.0 O B:ILE204 2.6 34.0 1.0 O B:LEU205 2.9 43.7 1.0 HA B:LEU205 3.2 42.0 1.0 C B:LEU205 3.3 44.0 1.0 C B:MET207 3.5 36.9 1.0 H B:MET207 3.6 40.3 1.0 C B:VAL210 3.6 29.5 1.0 H B:VAL210 3.6 36.9 1.0 HB2 B:MET207 3.7 44.1 1.0 C B:ILE204 3.7 35.5 1.0 CA B:LEU205 3.7 35.0 1.0 O B:HOH959 3.7 49.5 1.0 N B:MET207 3.8 33.5 1.0 HA B:HIS211 3.9 35.9 1.0 HB B:VAL210 4.0 37.6 1.0 CA B:MET207 4.1 35.0 1.0 HG21 B:ILE204 4.2 38.9 1.0 N B:LEU205 4.2 34.2 1.0 O B:HOH846 4.2 51.0 1.0 O B:HOH881 4.2 38.5 1.0 N B:ALA206 4.2 37.6 1.0 HG22 B:ILE204 4.3 38.9 1.0 N B:VAL210 4.3 30.7 1.0 CB B:MET207 4.3 36.7 1.0 C B:ALA206 4.4 34.8 1.0 CA B:VAL210 4.4 27.2 1.0 N B:HIS211 4.5 30.2 1.0 HA B:PRO208 4.6 38.1 1.0 N B:PRO208 4.7 37.9 1.0 CA B:HIS211 4.7 29.9 1.0 CG2 B:ILE204 4.7 32.4 1.0 CB B:VAL210 4.7 31.4 1.0 HD21 B:LEU205 4.7 57.8 1.0 H B:LEU212 4.7 37.0 1.0 CA B:ALA206 4.8 39.7 1.0 H B:ALA206 4.8 45.1 1.0 HB3 B:MET207 4.8 44.1 1.0 C B:PRO208 4.9 35.0 1.0 HA B:ALA206 4.9 47.6 1.0 CA B:PRO208 4.9 31.8 1.0 CA B:ILE204 4.9 39.7 1.0 HA B:ILE204 4.9 47.6 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