Sodium in PDB 9cya: C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine

All present enzymatic activity of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine:
4.1.1.116;

The structure of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine, PDB code: 9cya was solved by R.S.Phillips, S.Blankenship, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.82 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.387, 50.591, 73.308, 90, 120.88, 90
R / Rfree (%)	15.3 / 18.2

The structure of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine (pdb code 9cya). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine, PDB code: 9cya:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:25.7 occ:1.00 O A:VAL210 2.3 22.8 1.0 O A:HOH999 2.4 47.4 1.0 O A:ILE204 2.5 24.0 1.0 O A:MET207 2.5 23.8 1.0 O A:HOH990 2.9 22.6 1.0 HA A:LEU205 3.0 31.8 1.0 O A:LEU205 3.0 31.0 1.0 H A:MET207 3.4 27.0 1.0 C A:LEU205 3.4 28.2 1.0 C A:ILE204 3.5 22.8 1.0 CA A:LEU205 3.6 26.5 1.0 C A:MET207 3.6 23.9 1.0 HB2 A:MET207 3.6 24.2 1.0 C A:VAL210 3.6 20.1 1.0 N A:MET207 3.7 22.5 1.0 H A:VAL210 3.7 23.5 1.0 HA A:HIS211 3.8 21.2 1.0 HG22 A:ILE204 4.0 22.3 1.0 N A:LEU205 4.0 28.4 1.0 HB A:VAL210 4.1 19.2 1.0 CA A:MET207 4.1 20.9 1.0 HG23 A:ILE204 4.1 22.3 1.0 N A:ALA206 4.3 29.0 1.0 CB A:MET207 4.3 20.2 1.0 O A:HOH1049 4.3 52.0 1.0 N A:VAL210 4.4 19.6 1.0 H A:LEU212 4.4 20.8 1.0 CA A:VAL210 4.5 17.5 1.0 C A:ALA206 4.5 33.4 1.0 CG2 A:ILE204 4.5 18.6 1.0 N A:HIS211 4.5 17.2 1.0 HD23 A:LEU205 4.6 39.1 1.0 CA A:HIS211 4.6 17.6 1.0 N A:PRO208 4.7 21.9 1.0 HB3 A:MET207 4.7 24.2 1.0 CB A:VAL210 4.7 16.0 1.0 HA A:PRO208 4.7 28.2 1.0 H A:ALA206 4.8 34.7 1.0 CA A:ILE204 4.8 22.4 1.0 HA A:ILE204 4.8 26.9 1.0 H A:LEU205 4.8 34.1 1.0 CA A:ALA206 4.9 32.1 1.0 CB A:LEU205 4.9 31.5 1.0 HB3 A:LEU205 5.0 37.8 1.0

Sodium binding site 2 out of 2 in the C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:31.1 occ:1.00 OE1 A:GLU322 2.3 24.0 0.5 O A:HOH1010 2.4 57.0 1.0 O A:HOH945 2.5 32.9 1.0 OG1 A:THR46 2.5 21.2 1.0 O A:HOH667 2.6 30.7 1.0 OE1 A:GLU322 2.6 36.7 0.5 HG1 A:THR46 2.8 25.4 1.0 H A:THR46 2.9 29.1 1.0 CD A:GLU322 3.3 37.0 0.5 HB2 A:GLU322 3.3 22.7 0.5 HB2 A:GLU322 3.4 22.6 0.5 CD A:GLU322 3.4 39.2 0.5 HB3 A:GLU322 3.6 22.6 0.5 O A:HOH643 3.6 38.5 1.0 CB A:THR46 3.7 19.2 1.0 N A:THR46 3.8 24.3 1.0 HG23 A:THR46 3.8 26.6 1.0 HB3 A:GLU322 3.8 22.7 0.5 CB A:GLU322 3.9 18.8 0.5 CB A:GLU322 3.9 18.9 0.5 OE2 A:GLU322 4.0 30.9 0.5 HG21 A:THR46 4.0 26.6 1.0 CG2 A:THR46 4.0 22.2 1.0 HA A:PRO45 4.0 33.3 1.0 OE2 A:GLU322 4.1 28.6 0.5 OD2 A:ASP348 4.2 18.3 1.0 CG A:GLU322 4.2 20.8 0.5 O A:HOH676 4.2 46.6 1.0 CG A:GLU322 4.3 21.1 0.5 CA A:THR46 4.3 18.9 1.0 HB A:THR46 4.4 23.0 1.0 HG2 A:GLU322 4.6 24.9 0.5 O A:ALA41 4.7 29.7 1.0 O A:THR46 4.7 21.2 1.0 HG3 A:GLU322 4.8 25.4 0.5 O A:HOH728 4.8 35.2 0.8 C A:PRO45 4.8 25.4 1.0 CA A:PRO45 4.8 27.8 1.0 HG3 A:GLU322 4.9 24.9 0.5 C A:THR46 4.9 18.1 1.0 HG2 A:GLU322 5.0 25.4 0.5

R.S.Phillips, S.Blankenship. Structure of C387S Variant of D-Ornithine/D-Lysine Decarboxylase Complexed with Hepes and Putrescine To Be Published.