Sodium in PDB 2dkb: Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites

All present enzymatic activity of Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites:
4.1.1.64;

The structure of Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites, PDB code: 2dkb was solved by M.D.Toney, E.Hohenester, J.N.Jansonius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.700, 152.700, 86.600, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites (pdb code 2dkb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites, PDB code: 2dkb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Na435 b:31.1 occ:1.00 O A:HOH526 2.2 33.1 1.0 O A:LEU102 2.3 25.7 1.0 O A:ALA95 2.4 33.4 1.0 O A:PRO99 2.4 30.6 1.0 O A:THR98 2.5 28.1 1.0 OG1 A:THR98 2.6 17.2 1.0 C A:THR98 3.1 32.5 1.0 C A:PRO99 3.2 34.4 1.0 C A:LEU102 3.4 25.0 1.0 C A:ALA95 3.5 18.4 1.0 CB A:THR98 3.6 24.2 1.0 CB A:LEU102 3.7 17.1 1.0 N A:LEU102 3.8 30.5 1.0 CA A:THR98 3.8 20.8 1.0 N A:PRO99 3.8 30.0 1.0 CA A:LEU102 3.8 18.9 1.0 N A:THR98 3.9 19.7 1.0 CA A:ALA95 4.0 22.5 1.0 N A:PRO100 4.0 39.7 1.0 CA A:PRO99 4.0 19.7 1.0 CA A:PRO100 4.2 28.1 1.0 O A:LEU94 4.4 23.1 1.0 N A:ASP103 4.5 22.6 1.0 C A:PRO100 4.6 26.9 1.0 N A:ASN96 4.6 28.7 1.0 N A:GLY101 4.7 29.0 1.0 O A:HOH669 4.7 70.3 1.0 O A:HOH632 4.8 60.4 1.0 CB A:ALA95 4.8 19.0 1.0 C A:ASN96 4.9 40.5 1.0 CA A:ASN96 4.9 24.0 1.0 CG2 A:THR98 4.9 20.2 1.0 CG A:LEU102 4.9 20.1 1.0 CA A:ASP103 5.0 19.2 1.0 C A:ILE97 5.0 24.6 1.0

Sodium binding site 2 out of 2 in the Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Na436 b:29.4 occ:1.00 O A:HOH519 2.2 31.0 1.0 O A:HOH509 2.2 27.2 1.0 OD1 A:ASP307 2.3 24.6 1.0 O A:LEU78 2.4 28.1 1.0 O A:VAL305 2.6 20.7 1.0 CG A:ASP307 3.3 25.6 1.0 C A:LEU78 3.5 24.0 1.0 C A:VAL305 3.8 23.0 1.0 O A:SER306 3.9 27.4 1.0 C A:SER306 4.0 31.6 1.0 N A:SER80 4.0 21.6 1.0 CA A:SER80 4.0 31.8 1.0 O A:THR303 4.0 26.9 1.0 N A:ASP307 4.0 27.2 1.0 N A:LEU78 4.0 24.1 1.0 C A:PHE79 4.1 30.8 1.0 CA A:ASP307 4.1 22.3 1.0 OD2 A:ASP307 4.1 29.6 1.0 O A:PHE79 4.2 26.3 1.0 CA A:LEU78 4.2 24.0 1.0 C A:HIS304 4.3 28.5 1.0 CB A:ASP307 4.3 19.6 1.0 N A:VAL305 4.3 16.4 1.0 CE1 A:HIS77 4.4 22.7 1.0 ND1 A:HIS77 4.5 24.6 1.0 N A:PHE79 4.5 23.4 1.0 CG1 A:VAL305 4.5 19.7 1.0 O A:HIS304 4.5 22.0 1.0 CB A:SER306 4.6 18.4 1.0 CB A:LEU78 4.6 17.1 1.0 CA A:HIS304 4.6 25.4 1.0 CA A:SER306 4.6 18.1 1.0 CA A:VAL305 4.7 22.1 1.0 N A:SER306 4.7 22.1 1.0 CB A:SER80 4.7 29.2 1.0 CA A:PHE79 4.7 25.7 1.0 C A:THR303 5.0 22.5 1.0

M.D.Toney, E.Hohenester, S.W.Cowan, J.N.Jansonius. Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Sites. Science V. 261 756 1993.
ISSN: ISSN 0036-8075
PubMed: 8342040