Magnesium in PDB 4hcl: Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Lyxarohydroxamate

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium and L-Lyxarohydroxamate, PDB code: 4hcl 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)	37.40 / 1.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	118.260, 118.260, 133.342, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.7

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


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-Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:22.2 occ:1.00 OE1 A:GLU258 2.0 22.5 1.0 O A:HOH767 2.0 23.0 1.0 OE2 A:GLU232 2.0 23.5 1.0 O1 A:LLH403 2.1 26.0 1.0 OD1 A:ASP206 2.1 23.9 1.0 ON A:LLH403 2.2 26.1 1.0 C1 A:LLH403 2.8 36.1 1.0 N A:LLH403 2.8 27.8 1.0 CD A:GLU258 3.0 27.0 1.0 CD A:GLU232 3.1 24.0 1.0 CG A:ASP206 3.1 24.0 1.0 OE2 A:GLU258 3.4 25.6 1.0 OD2 A:ASP206 3.5 24.2 1.0 CG A:GLU232 3.9 19.4 1.0 NH1 A:ARG280 3.9 21.1 1.0 NZ A:LYS169 3.9 20.4 1.0 OE1 A:GLU232 4.0 23.0 1.0 NE A:ARG280 4.0 19.0 1.0 NE2 A:HIS171 4.2 27.5 1.0 O4 A:LLH403 4.2 35.7 1.0 CG A:GLU258 4.3 21.9 1.0 C2 A:LLH403 4.3 39.9 1.0 OE2 A:GLU233 4.3 24.3 1.0 CB A:ASP206 4.4 20.7 1.0 NH1 B:ARG90 4.4 31.2 1.0 CZ A:ARG280 4.5 21.2 1.0 CD2 A:HIS309 4.5 25.0 1.0 CB A:GLU258 4.5 21.1 1.0 CE A:LYS169 4.8 23.5 1.0 O3 A:LLH403 4.9 45.1 1.0 CD2 A:HIS171 4.9 30.6 1.0 NE2 A:HIS309 4.9 26.4 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-Lyxarohydroxamate


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-Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.8 occ:1.00 O A:LEU250 2.1 19.8 1.0 O A:SER247 2.1 18.9 1.0 O A:HOH783 2.1 24.7 1.0 O A:HOH517 2.1 22.1 1.0 O A:HOH507 2.2 20.0 1.0 O A:HOH513 2.2 21.7 1.0 C A:SER247 3.2 18.7 1.0 C A:LEU250 3.3 21.2 1.0 CA A:SER247 3.9 16.7 1.0 OD2 A:ASP277 4.1 18.6 1.0 O A:HOH688 4.2 34.4 1.0 N A:LEU250 4.2 18.7 1.0 CA A:LEU250 4.2 17.0 1.0 OD1 A:ASP277 4.2 21.1 1.0 N A:ASP251 4.2 18.2 1.0 O A:HOH577 4.2 32.7 1.0 CA A:ASP251 4.3 19.3 1.0 N A:ASP248 4.3 19.5 1.0 O A:ASP251 4.4 22.1 1.0 O A:ILE252 4.4 18.6 1.0 C A:ASP251 4.4 22.0 1.0 C A:ASP248 4.5 22.4 1.0 CB A:LEU250 4.5 17.6 1.0 CB A:SER247 4.5 19.8 1.0 CA A:ASP248 4.5 20.1 1.0 CG A:ASP277 4.5 23.7 1.0 O A:ASP248 4.6 23.0 1.0 O A:HOH738 4.8 36.9 1.0 C A:ASN249 4.9 25.0 1.0 N A:ASN249 4.9 19.0 1.0 O A:LEU246 5.0 16.8 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-Lyxarohydroxamate


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-Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:23.5 occ:1.00 OE1 B:GLU258 2.0 21.4 1.0 O B:HOH770 2.0 24.1 1.0 OE2 B:GLU232 2.1 21.8 1.0 O1 B:LLH403 2.1 27.3 1.0 OD1 B:ASP206 2.1 25.3 1.0 ON B:LLH403 2.2 26.6 1.0 C1 B:LLH403 2.8 36.8 1.0 N B:LLH403 2.8 26.8 1.0 CD B:GLU258 3.0 25.3 1.0 CG B:ASP206 3.1 22.8 1.0 CD B:GLU232 3.1 21.8 1.0 OE2 B:GLU258 3.4 25.3 1.0 OD2 B:ASP206 3.5 23.2 1.0 CG B:GLU232 3.8 20.0 1.0 NH1 B:ARG280 3.9 20.2 1.0 NZ B:LYS169 3.9 22.1 1.0 OE1 B:GLU232 4.0 22.1 1.0 NE B:ARG280 4.0 19.7 1.0 O4 B:LLH403 4.1 37.7 1.0 NE2 B:HIS171 4.1 28.3 1.0 CG B:GLU258 4.2 24.0 1.0 C2 B:LLH403 4.3 38.2 1.0 OE2 B:GLU233 4.4 24.9 1.0 CB B:ASP206 4.4 22.4 1.0 CZ B:ARG280 4.4 20.7 1.0 NH1 A:ARG90 4.5 30.2 1.0 CB B:GLU258 4.5 20.9 1.0 CD2 B:HIS309 4.6 25.1 1.0 CE B:LYS169 4.8 22.2 1.0 CD2 B:HIS171 4.9 32.4 1.0 O3 B:LLH403 4.9 45.6 1.0 NE2 B:HIS309 5.0 24.1 1.0 C3 B:LLH403 5.0 40.5 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-Lyxarohydroxamate


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-Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:21.7 occ:1.00 O B:LEU250 2.0 20.2 1.0 O B:HOH788 2.1 25.6 1.0 O B:SER247 2.1 21.1 1.0 O B:HOH512 2.2 21.4 1.0 O B:HOH515 2.2 20.8 1.0 O B:HOH517 2.2 21.7 1.0 C B:LEU250 3.3 21.3 1.0 C B:SER247 3.3 19.5 1.0 CA B:SER247 3.9 18.9 1.0 OD2 B:ASP277 4.1 19.5 1.0 O B:HOH701 4.1 35.1 1.0 N B:LEU250 4.2 18.9 1.0 CA B:LEU250 4.2 18.3 1.0 OD1 B:ASP277 4.2 21.6 1.0 N B:ASP251 4.2 18.7 1.0 O B:HOH598 4.2 32.5 1.0 CA B:ASP251 4.2 19.7 1.0 O B:ASP251 4.3 21.8 1.0 N B:ASP248 4.3 20.1 1.0 O B:ILE252 4.4 18.2 1.0 C B:ASP251 4.4 22.4 1.0 C B:ASP248 4.5 21.5 1.0 CB B:SER247 4.5 20.9 1.0 CG B:ASP277 4.5 22.8 1.0 CB B:LEU250 4.5 19.7 1.0 CA B:ASP248 4.6 21.3 1.0 O B:ASP248 4.6 23.1 1.0 C B:ASN249 4.9 25.9 1.0 N B:ASN249 4.9 19.8 1.0 O B:LEU246 5.0 18.8 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-Lyxarohydroxamate To Be Published.