Sodium in PDB 4hcd: Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, PDB code: 4hcd was solved by A.A.Fedorov, E.V.Fedorov, A.Sakai, C.Millikin, 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)	24.91 / 1.70
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	118.733, 118.733, 133.199, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.5

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

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium (pdb code 4hcd). 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, PDB code: 4hcd:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:19.4 occ:1.00 O A:HOH773 2.2 21.0 1.0 O A:HOH724 2.3 18.4 1.0 O A:HOH551 2.3 12.6 1.0 O A:GLY274 2.4 9.5 1.0 OG A:SER247 2.5 7.1 0.6 O A:HOH722 2.6 27.2 1.0 CB A:SER247 3.2 9.3 0.4 CB A:SER247 3.3 9.2 0.6 C A:GLY274 3.5 9.6 1.0 OD2 A:ASP248 3.6 24.3 1.0 OG A:SER247 4.1 7.6 0.4 O A:HOH875 4.1 24.4 1.0 CD A:LYS244 4.1 15.7 0.4 CA A:GLY274 4.2 10.5 1.0 C A:SER247 4.2 7.6 0.6 C A:SER247 4.2 7.6 0.4 N A:ASP248 4.3 7.6 1.0 O A:LYS244 4.3 6.8 0.6 O A:LYS244 4.3 6.8 0.4 O A:HOH786 4.3 13.2 1.0 CA A:SER247 4.3 6.2 0.4 CE A:LYS244 4.3 8.4 0.4 CA A:SER247 4.4 6.1 0.6 CG A:ASP248 4.5 26.6 1.0 N A:ALA275 4.6 5.4 1.0 O A:SER247 4.7 8.0 0.6 O A:SER247 4.7 8.0 0.4 OD1 A:ASP277 4.7 7.7 1.0 CA A:ALA275 4.8 5.1 1.0 C A:ALA275 4.9 8.1 1.0 N A:CYS276 4.9 7.4 1.0 CA A:ASP248 4.9 9.4 1.0 O A:HOH915 4.9 32.6 1.0 CA A:LYS244 5.0 5.6 0.6 CA A:LYS244 5.0 5.6 0.4

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:8.1 occ:1.00 OD2 A:ASP206 2.2 7.0 1.0 O A:ALA207 2.2 6.4 1.0 O A:GLU233 2.3 4.7 1.0 ND1 A:HIS209 2.5 6.9 1.0 O A:GLU232 2.8 4.3 1.0 C A:GLU233 3.1 5.1 1.0 CE1 A:HIS209 3.1 5.8 1.0 C A:ALA207 3.4 6.0 1.0 CB A:GLU233 3.4 5.4 1.0 N A:ALA207 3.4 6.6 1.0 CG A:ASP206 3.5 7.5 1.0 C A:ASP206 3.6 7.7 1.0 CG A:HIS209 3.6 5.5 1.0 CA A:GLU233 3.7 4.9 1.0 C A:GLU232 3.8 3.0 1.0 CA A:HIS209 3.9 5.3 1.0 O A:HOH966 3.9 6.4 1.0 CA A:ASP206 4.0 6.3 1.0 CA A:ALA207 4.0 10.2 1.0 CG A:GLU233 4.0 6.6 1.0 N A:PRO234 4.1 5.7 1.0 N A:HIS209 4.1 6.2 1.0 CB A:HIS209 4.1 5.3 1.0 O A:ASP206 4.1 7.2 1.0 C A:PHE208 4.2 8.1 1.0 N A:GLU233 4.2 5.9 1.0 O A:PHE208 4.3 6.5 1.0 CB A:ASP206 4.3 6.3 1.0 NE2 A:HIS209 4.3 5.3 1.0 O A:HOH707 4.3 14.5 1.0 OD1 A:ASP206 4.3 8.0 1.0 CA A:PRO234 4.4 3.5 1.0 N A:PHE208 4.5 5.0 1.0 CD2 A:HIS209 4.6 5.1 1.0 CD A:GLU233 4.7 9.1 1.0 OE2 A:GLU233 4.8 6.9 1.0 CE A:MSE174 4.8 9.3 1.0 CA A:PHE208 4.8 6.7 1.0 CB A:ALA207 5.0 11.3 1.0

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