Sodium in PDB 4v15: Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans

All present enzymatic activity of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans:
4.1.2.42;

The structure of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans, PDB code: 4v15 was solved by M.K.Uhl, G.Oberdorfer, G.Steinkellner, L.Riegler, M.Schuermann, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.759 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.267, 84.278, 72.852, 90.00, 111.90, 90.00
R / Rfree (%)	14.84 / 17.67

The structure of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans (pdb code 4v15). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans, PDB code: 4v15:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1383 b:15.8 occ:1.00 O A:LEU179 2.2 13.1 1.0 O A:HOH2298 2.2 27.6 1.0 O A:LEU176 2.3 16.8 1.0 O A:ALA173 2.5 15.6 1.0 O A:ARG174 2.6 16.1 1.0 O A:HOH2299 2.8 24.1 1.0 C A:ARG174 3.2 15.0 1.0 C A:LEU179 3.3 13.0 1.0 C A:LEU176 3.5 17.8 1.0 C A:ALA173 3.6 14.0 1.0 N A:LEU176 3.6 14.8 1.0 O A:HOH2300 3.7 47.2 1.0 CA A:ARG174 3.7 12.7 1.0 O A:HOH2261 3.8 41.4 1.0 C A:ALA175 4.0 12.6 1.0 N A:ALA175 4.0 11.7 1.0 CA A:LEU179 4.1 11.3 1.0 CA A:LEU176 4.1 15.2 1.0 N A:LEU179 4.1 12.1 1.0 N A:ARG174 4.1 12.5 1.0 CB A:LEU179 4.2 11.1 1.0 O A:HOH2304 4.2 29.1 1.0 N A:ASN180 4.3 11.5 1.0 CA A:ALA175 4.5 11.6 1.0 O A:PRO177 4.5 18.1 0.2 CA A:ASN180 4.5 12.9 1.0 N A:PRO177 4.5 19.5 0.2 O A:ALA175 4.5 14.7 1.0 N A:PRO177 4.6 19.2 0.8 OD1 A:ASN180 4.6 31.6 1.0 C A:PRO177 4.6 18.3 0.2 O A:HOH2305 4.7 15.9 1.0 CB A:LEU176 4.8 14.8 1.0 CA A:PRO177 4.8 21.7 0.2 CA A:PRO177 4.8 22.2 0.8 CA A:ALA173 4.8 13.7 1.0 O A:GLN172 5.0 12.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1383 b:18.7 occ:1.00 O B:LEU179 2.2 13.4 1.0 O B:HOH2262 2.3 33.9 1.0 O B:LEU176 2.4 21.6 1.0 O B:ALA173 2.5 16.2 1.0 O B:ARG174 2.5 19.2 1.0 O B:HOH2261 2.8 25.9 1.0 C B:ARG174 3.2 13.4 1.0 C B:LEU179 3.3 12.2 1.0 C B:LEU176 3.5 25.5 1.0 C B:ALA173 3.6 14.5 1.0 N B:LEU176 3.6 15.7 1.0 CA B:ARG174 3.7 15.0 1.0 C B:ALA175 4.0 15.3 1.0 N B:ALA175 4.0 13.5 1.0 CA B:LEU176 4.1 18.1 1.0 N B:ARG174 4.1 13.7 1.0 CA B:LEU179 4.1 12.1 1.0 N B:LEU179 4.2 16.3 1.0 O B:PRO177 4.2 28.8 0.3 O B:HOH2267 4.3 26.7 1.0 CB B:LEU179 4.3 11.9 1.0 N B:ASN180 4.3 16.3 1.0 ND2 B:ASN180 4.4 26.0 1.0 CA B:ALA175 4.5 13.9 1.0 CA B:ASN180 4.5 14.8 1.0 O B:HOH2268 4.5 16.4 1.0 N B:PRO177 4.6 27.2 0.3 N B:PRO177 4.6 27.3 0.7 O B:ALA175 4.6 16.6 1.0 C B:PRO177 4.6 25.4 0.3 CB B:LEU176 4.8 20.9 1.0 O B:HOH2263 4.8 38.7 1.0 CA B:ALA173 4.8 14.2 1.0 CA B:PRO177 4.9 26.6 0.7 CA B:PRO177 4.9 27.9 0.3

M.K.Uhl, G.Oberdorfer, G.Steinkellner, L.Riegler, M.Schuermann, K.Gruber. The Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans Provides Insight Into A Metal Ion Assisted Plp-Dependent Mechanism To Be Published.