Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Tartrate, PDB code: 4hch:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg405 b:11.4 occ:1.00 OE1 A:GLU258 2.0 12.8 1.0 OD1 A:ASP206 2.0 13.4 1.0 OE2 A:GLU232 2.0 11.3 1.0 O A:HOH952 2.0 13.1 1.0 O A:HOH950 2.1 12.2 1.0 O A:HOH951 2.2 13.0 1.0 CD A:GLU258 3.0 14.2 1.0 CG A:ASP206 3.0 12.8 1.0 CD A:GLU232 3.1 15.2 1.0 OE2 A:GLU258 3.4 13.7 1.0 OD2 A:ASP206 3.6 13.7 1.0 CG A:GLU232 3.8 11.2 1.0 NH1 A:ARG280 4.0 10.3 1.0 OE1 A:GLU232 4.0 12.4 1.0 NZ A:LYS169 4.0 9.9 1.0 NE2 A:HIS171 4.1 12.9 1.0 NH1 B:ARG90 4.2 13.2 1.0 NE A:ARG280 4.2 11.0 1.0 CB A:ASP206 4.2 10.9 1.0 CG A:GLU258 4.3 10.9 1.0 O3 A:TLA401 4.3 18.5 1.0 OE2 A:GLU233 4.5 11.9 1.0 O1 A:GOL402 4.5 14.7 1.0 CB A:GLU258 4.5 11.9 1.0 CZ A:ARG280 4.6 10.7 1.0 CD2 A:HIS309 4.6 12.5 1.0 CD2 A:HIS171 4.7 13.7 1.0 CE1 A:HIS209 4.7 12.1 1.0 NE2 A:HIS309 4.8 11.8 1.0 CE A:LYS169 4.9 10.2 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 A:Mg406 b:13.3 occ:1.00 O A:LEU250 2.0 13.5 1.0 O A:HOH966 2.1 16.0 1.0 O A:SER247 2.1 12.7 1.0 O A:HOH949 2.1 11.2 1.0 O A:HOH965 2.1 18.9 1.0 O A:HOH964 2.1 14.5 1.0 C A:LEU250 3.3 12.2 1.0 C A:SER247 3.3 13.8 1.0 CA A:SER247 4.0 9.9 1.0 OD2 A:ASP277 4.0 11.1 1.0 N A:LEU250 4.2 11.8 1.0 CA A:LEU250 4.2 12.2 1.0 OD1 A:ASP277 4.2 13.2 1.0 N A:ASP251 4.2 13.6 1.0 O A:HOH703 4.2 28.1 1.0 O A:HOH643 4.2 22.1 1.0 CA A:ASP251 4.3 14.2 1.0 O A:ASP251 4.3 14.0 1.0 N A:ASP248 4.3 13.0 1.0 O A:ILE252 4.4 10.8 1.0 C A:ASP251 4.4 12.4 1.0 CG A:ASP277 4.5 14.6 1.0 CB A:SER247 4.5 13.9 1.0 CB A:LEU250 4.5 11.4 1.0 CA A:ASP248 4.5 13.4 1.0 C A:ASP248 4.6 15.5 1.0 O A:ASP248 4.8 16.6 1.0 O A:LEU246 5.0 11.1 1.0 N A:ASN249 5.0 13.4 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg406 b:11.2 occ:1.00 OE2 B:GLU232 2.0 11.9 1.0 OE1 B:GLU258 2.0 11.4 1.0 OD1 B:ASP206 2.0 13.7 1.0 O B:HOH940 2.1 12.7 1.0 O B:HOH938 2.1 14.2 1.0 O B:HOH937 2.1 12.7 1.0 CD B:GLU258 3.0 14.3 1.0 CG B:ASP206 3.1 11.8 1.0 CD B:GLU232 3.1 13.5 1.0 OE2 B:GLU258 3.4 12.5 1.0 OD2 B:ASP206 3.6 12.3 1.0 CG B:GLU232 3.8 10.4 1.0 NH1 B:ARG280 4.0 11.5 1.0 NZ B:LYS169 4.0 9.7 1.0 OE1 B:GLU232 4.0 11.9 1.0 NE2 B:HIS171 4.0 11.5 1.0 NE B:ARG280 4.2 11.5 1.0 CB B:ASP206 4.2 11.4 1.0 CG B:GLU258 4.2 11.6 1.0 NH1 A:ARG90 4.2 14.8 1.0 O3 B:TLA401 4.3 17.6 1.0 O1 B:GOL404 4.4 16.4 1.0 OE2 B:GLU233 4.5 11.8 1.0 CB B:GLU258 4.5 11.5 1.0 CZ B:ARG280 4.6 11.8 1.0 CD2 B:HIS309 4.6 14.0 1.0 CD2 B:HIS171 4.7 14.7 1.0 CE1 B:HIS209 4.7 9.7 1.0 CE B:LYS169 4.8 11.2 1.0 NE2 B:HIS309 4.9 12.4 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg407 b:13.3 occ:1.00 O B:LEU250 2.0 14.9 1.0 O B:SER247 2.1 12.5 1.0 O B:HOH941 2.1 14.8 1.0 O B:HOH936 2.1 11.6 1.0 O B:HOH942 2.1 19.4 1.0 O B:HOH939 2.1 15.7 1.0 C B:SER247 3.2 13.1 1.0 C B:LEU250 3.2 12.9 1.0 CA B:SER247 3.9 10.3 1.0 OD2 B:ASP277 4.1 10.2 1.0 N B:LEU250 4.1 11.9 1.0 CA B:LEU250 4.1 12.2 1.0 OD1 B:ASP277 4.2 15.0 1.0 O B:HOH643 4.2 22.4 1.0 N B:ASP251 4.2 11.5 1.0 CA B:ASP251 4.2 12.4 1.0 O B:HOH710 4.3 25.4 1.0 N B:ASP248 4.3 15.2 1.0 O B:ASP251 4.3 15.6 1.0 O B:ILE252 4.4 11.4 1.0 C B:ASP251 4.4 11.4 1.0 CB B:SER247 4.5 13.1 1.0 CG B:ASP277 4.5 15.2 1.0 CB B:LEU250 4.5 11.9 1.0 CA B:ASP248 4.5 14.2 1.0 C B:ASP248 4.6 16.7 1.0 O B:ASP248 4.7 17.6 1.0 O B:LEU246 4.9 12.1 1.0 N B:ASN249 5.0 13.5 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.