Sodium in PDB 4hch: Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate, PDB code: 4hch was solved by A.A.Fedorov, E.V.Fedorov, A.Sakai, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.79 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	118.252, 118.252, 133.018, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 17.1

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate (pdb code 4hch). 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-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate, PDB code: 4hch:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate


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-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:13.1 occ:1.00 O A:ALA207 2.2 10.9 1.0 OD2 A:ASP206 2.2 13.7 1.0 O A:GLU233 2.3 10.6 1.0 ND1 A:HIS209 2.5 13.2 1.0 O A:GLU232 2.9 11.3 1.0 C A:GLU233 3.0 10.1 1.0 CE1 A:HIS209 3.1 12.1 1.0 C A:ALA207 3.3 10.9 1.0 N A:ALA207 3.3 11.6 1.0 CB A:GLU233 3.3 11.5 1.0 CG A:ASP206 3.5 12.8 1.0 C A:ASP206 3.6 14.7 1.0 CA A:GLU233 3.6 9.7 1.0 CG A:HIS209 3.6 10.8 1.0 C A:GLU232 3.8 9.4 1.0 CA A:HIS209 3.9 12.7 1.0 CA A:ALA207 3.9 13.6 1.0 CG A:GLU233 3.9 10.0 1.0 CA A:ASP206 3.9 11.5 1.0 O A:HOH952 4.0 13.1 1.0 N A:PRO234 4.0 11.0 1.0 N A:GLU233 4.1 10.9 1.0 N A:HIS209 4.1 12.9 1.0 C A:PHE208 4.2 13.5 1.0 CB A:HIS209 4.2 10.9 1.0 O A:HOH690 4.2 22.5 1.0 O A:PHE208 4.2 13.2 1.0 O A:ASP206 4.2 11.3 1.0 NE2 A:HIS209 4.2 11.3 1.0 CB A:ASP206 4.3 10.9 1.0 CA A:PRO234 4.3 10.1 1.0 OD1 A:ASP206 4.4 13.4 1.0 N A:PHE208 4.4 10.0 1.0 CD2 A:HIS209 4.5 12.7 1.0 CD A:GLU233 4.7 11.1 1.0 CA A:PHE208 4.8 13.1 1.0 OE2 A:GLU233 4.8 11.9 1.0 CB A:ALA207 4.9 16.3 1.0 CE A:MET174 5.0 14.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate


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-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:13.7 occ:1.00 O B:ALA207 2.2 11.2 1.0 OD2 B:ASP206 2.2 12.3 1.0 O B:GLU233 2.2 10.7 1.0 ND1 B:HIS209 2.5 13.0 1.0 O B:GLU232 2.8 10.4 1.0 C B:GLU233 3.0 11.4 1.0 CE1 B:HIS209 3.0 9.7 1.0 C B:ALA207 3.3 11.2 1.0 N B:ALA207 3.3 11.8 1.0 CB B:GLU233 3.3 11.9 1.0 CG B:ASP206 3.5 11.8 1.0 CA B:GLU233 3.6 10.1 1.0 CG B:HIS209 3.6 12.2 1.0 C B:ASP206 3.6 16.6 1.0 C B:GLU232 3.8 10.1 1.0 CA B:HIS209 3.9 12.0 1.0 CA B:ALA207 3.9 13.2 1.0 CG B:GLU233 4.0 9.8 1.0 CA B:ASP206 4.0 11.8 1.0 O B:HOH940 4.0 12.7 1.0 N B:PRO234 4.0 10.5 1.0 N B:GLU233 4.1 11.1 1.0 N B:HIS209 4.1 11.1 1.0 CB B:HIS209 4.2 10.0 1.0 C B:PHE208 4.2 13.1 1.0 O B:ASP206 4.2 12.2 1.0 NE2 B:HIS209 4.2 12.1 1.0 O B:PHE208 4.2 11.7 1.0 O B:HOH701 4.2 21.6 1.0 CB B:ASP206 4.3 11.4 1.0 CA B:PRO234 4.3 8.9 1.0 OD1 B:ASP206 4.4 13.7 1.0 N B:PHE208 4.4 10.0 1.0 CD2 B:HIS209 4.5 11.1 1.0 CD B:GLU233 4.7 11.9 1.0 OE2 B:GLU233 4.8 11.8 1.0 CA B:PHE208 4.8 11.8 1.0 CB B:ALA207 4.9 16.2 1.0 CE B:MET174 5.0 13.4 1.0

A.A.Fedorov, E.V.Fedorov, A.Sakai, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate To Be Published.