Sodium in PDB 4pfm: Shewanella Benthica Dhdps with Lysine and Pyruvate

All present enzymatic activity of Shewanella Benthica Dhdps with Lysine and Pyruvate:
4.3.3.7;

The structure of Shewanella Benthica Dhdps with Lysine and Pyruvate, PDB code: 4pfm was solved by J.M.Wubben, J.J.Paxman, C.Dogovski, S.Panjikar, M.A.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.273, 83.929, 143.868, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 20.6

The binding sites of Sodium atom in the Shewanella Benthica Dhdps with Lysine and Pyruvate (pdb code 4pfm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Shewanella Benthica Dhdps with Lysine and Pyruvate, PDB code: 4pfm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Shewanella Benthica Dhdps with Lysine and Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Shewanella Benthica Dhdps with Lysine and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:60.8 occ:1.00 O A:HOH538 2.3 50.1 1.0 O A:VAL152 2.4 53.6 1.0 O A:ILE157 2.5 42.7 1.0 O A:VAL154 2.7 56.3 1.0 C A:ILE157 3.5 41.7 1.0 C A:VAL152 3.6 53.6 1.0 O A:HOH544 3.7 65.8 1.0 C A:VAL154 3.8 57.1 1.0 O A:PRO155 3.9 55.5 1.0 CA A:VAL152 4.2 50.9 1.0 C A:PRO155 4.2 55.0 1.0 CA A:PRO155 4.3 56.0 1.0 N A:ILE157 4.3 42.4 1.0 CA A:ILE157 4.3 41.3 1.0 N A:ILE158 4.4 41.4 1.0 CA A:ILE158 4.4 41.0 1.0 CG1 A:VAL152 4.5 47.5 1.0 CE1 A:PHE181 4.5 47.6 1.0 CD1 A:PHE181 4.6 44.9 1.0 N A:PRO155 4.6 57.1 1.0 N A:GLU153 4.6 55.0 1.0 C A:GLU153 4.7 58.5 1.0 N A:VAL154 4.7 58.1 1.0 O A:LEU151 4.8 48.2 1.0 CB A:ILE157 4.8 41.3 1.0 CA A:VAL154 4.9 56.3 1.0 CA A:GLU153 5.0 58.4 1.0 O A:GLU153 5.0 59.6 1.0 CB A:VAL152 5.0 51.3 1.0 N A:ASN156 5.0 51.0 1.0

Sodium binding site 2 out of 2 in the Shewanella Benthica Dhdps with Lysine and Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Shewanella Benthica Dhdps with Lysine and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:63.9 occ:1.00 O B:VAL152 2.4 51.3 1.0 O B:ILE157 2.5 44.9 1.0 O B:HOH540 2.6 59.3 1.0 O B:VAL154 2.7 56.1 1.0 C B:ILE157 3.5 44.4 1.0 C B:VAL152 3.6 51.3 1.0 O B:PRO155 3.7 55.3 1.0 C B:VAL154 3.8 55.8 1.0 C B:PRO155 4.0 54.8 1.0 N B:ILE157 4.1 45.6 1.0 CA B:PRO155 4.2 55.9 1.0 CA B:VAL152 4.3 50.0 1.0 CA B:ILE157 4.3 43.8 1.0 N B:ILE158 4.4 44.1 1.0 CA B:ILE158 4.5 44.2 1.0 N B:PRO155 4.6 56.6 1.0 N B:VAL154 4.6 55.1 1.0 C B:GLU153 4.6 56.2 1.0 CG1 B:VAL152 4.6 45.6 1.0 CE1 B:PHE181 4.7 48.6 1.0 N B:GLU153 4.7 52.7 1.0 O B:LEU151 4.7 46.7 1.0 N B:ASN156 4.7 52.3 1.0 CB B:ILE157 4.7 44.1 1.0 O B:HOH458 4.8 66.8 1.0 CD1 B:PHE181 4.8 47.5 1.0 CA B:VAL154 4.8 54.5 1.0 O B:GLU153 4.9 57.3 1.0 CA B:GLU153 4.9 56.5 1.0 C B:ASN156 5.0 47.0 1.0

J.M.Wubben, J.J.Paxman, C.Dogovski, S.Panjikar, M.A.Perugini. Defining A Molecular Determinant of Lysine-Mediated Allosteric Inhibition of Dhdps. To Be Published.