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

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate, PDB code: 4mmw 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)	49.10 / 1.65
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	118.099, 118.099, 133.278, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.4

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

Chlorine

(Cl)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate (pdb code 4mmw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate, PDB code: 4mmw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate 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, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.8 occ:1.00 O A:HOH857 2.1 31.6 1.0 O A:HOH854 2.2 39.7 1.0 O A:PRO335 2.2 17.6 1.0 O A:HOH698 2.3 29.4 1.0 O A:HOH669 2.3 31.8 1.0 O A:HOH859 2.4 44.4 1.0 C A:PRO335 3.3 20.2 1.0 O A:HOH763 3.8 35.3 1.0 CA A:PRO335 3.9 18.2 1.0 OE2 A:GLU338 4.2 60.0 1.0 N A:PHE336 4.5 18.7 1.0 CB A:PRO335 4.5 19.4 1.0 O A:LEU337 4.7 27.5 1.0 O A:HOH515 4.7 17.2 1.0 CA A:PHE336 4.8 17.6 1.0 C A:PHE336 4.9 19.6 1.0 N A:LEU337 5.0 19.6 1.0 O A:HIS334 5.0 17.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate 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, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.9 occ:1.00 OH5 A:XYH404 2.0 16.6 0.4 OE1 A:GLU258 2.0 15.2 1.0 OE2 A:GLU232 2.0 15.5 1.0 ON A:LLH405 2.0 13.7 0.5 OD1 A:ASP206 2.1 19.1 1.0 O A:HOH794 2.1 16.3 1.0 O1 A:LLH405 2.2 16.3 0.5 OH6 A:XYH404 2.4 16.8 0.4 N A:LLH405 2.8 13.1 0.5 C1 A:LLH405 2.8 15.4 0.5 C5 A:XYH404 2.9 16.8 0.4 CD A:GLU258 3.0 18.6 1.0 CD A:GLU232 3.1 18.1 1.0 CG A:ASP206 3.1 16.3 1.0 N6 A:XYH404 3.1 12.3 0.4 OE2 A:GLU258 3.4 17.3 1.0 OD2 A:ASP206 3.5 15.4 1.0 CG A:GLU232 3.9 13.8 1.0 NH1 A:ARG280 3.9 15.2 1.0 NZ A:LYS169 3.9 12.2 1.0 OE1 A:GLU232 4.0 16.3 1.0 NE A:ARG280 4.0 15.1 1.0 OH2 A:XYH404 4.0 25.1 0.4 NE2 A:HIS171 4.1 18.6 1.0 O4 A:LLH405 4.2 23.9 0.5 CG A:GLU258 4.3 14.2 1.0 C2 A:LLH405 4.3 19.4 0.5 CB A:ASP206 4.3 14.2 1.0 NH1 B:ARG90 4.4 22.7 1.0 C4 A:XYH404 4.4 21.4 0.4 CZ A:ARG280 4.4 14.7 1.0 OE2 A:GLU233 4.4 17.3 1.0 CB A:GLU258 4.5 13.2 1.0 O3 A:LLH405 4.6 23.8 0.5 CD2 A:HIS309 4.7 19.4 1.0 CE A:LYS169 4.7 13.4 1.0 OH4 A:XYH404 4.7 18.3 0.4 CD2 A:HIS171 4.9 18.7 1.0 C3 A:LLH405 4.9 24.5 0.5 CE1 A:HIS209 5.0 16.7 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate 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, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.5 occ:1.00 O A:LEU250 2.0 17.3 1.0 O A:SER247 2.1 15.7 0.3 O A:HOH796 2.1 16.6 1.0 O A:SER247 2.1 15.4 0.7 O A:HOH797 2.1 16.1 1.0 O A:HOH798 2.2 18.1 1.0 O A:HOH795 2.2 16.5 1.0 C A:SER247 3.2 15.0 0.3 C A:SER247 3.2 15.3 0.7 C A:LEU250 3.3 17.3 1.0 CA A:SER247 3.9 14.5 0.3 CA A:SER247 4.0 14.3 0.7 O A:HOH678 4.1 37.3 1.0 OD2 A:ASP277 4.1 14.6 1.0 N A:LEU250 4.2 15.6 1.0 CA A:LEU250 4.2 14.8 1.0 N A:ASP251 4.2 17.2 1.0 CA A:ASP251 4.2 17.3 1.0 O A:HOH655 4.3 25.6 1.0 OD1 A:ASP277 4.3 17.1 1.0 N A:ASP248 4.3 14.8 1.0 O A:ASP251 4.3 18.0 1.0 C A:ASP251 4.4 15.9 1.0 O A:ILE252 4.4 12.9 1.0 C A:ASP248 4.5 20.6 1.0 CB A:SER247 4.5 15.2 0.3 CA A:ASP248 4.5 18.0 1.0 CB A:LEU250 4.6 13.0 1.0 CB A:SER247 4.6 16.2 0.7 CG A:ASP277 4.6 14.8 1.0 O A:ASP248 4.6 20.2 1.0 O A:HOH802 4.8 27.3 1.0 N A:ASN249 4.9 13.8 1.0 C A:ASN249 4.9 20.5 1.0 O A:LEU246 4.9 13.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate 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, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:22.2 occ:0.54 O B:HOH842 2.0 40.2 1.0 O B:HOH856 2.0 32.4 1.0 O B:HOH804 2.1 35.8 1.0 O B:PRO335 2.2 17.4 1.0 O B:HOH676 2.3 32.1 1.0 O B:HOH857 2.4 34.8 1.0 C B:PRO335 3.3 17.7 1.0 O B:HOH693 3.7 39.1 1.0 O B:HOH831 3.9 36.8 1.0 CA B:PRO335 3.9 16.6 1.0 N B:PHE336 4.4 19.1 1.0 CB B:PRO335 4.5 19.9 1.0 OE1 B:GLU338 4.5 66.5 1.0 O B:LEU337 4.6 28.2 1.0 O B:HOH509 4.7 17.7 1.0 CA B:PHE336 4.8 16.9 1.0 C B:PHE336 4.9 19.7 1.0 N B:LEU337 5.0 19.4 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:14.2 occ:0.94 OE2 B:GLU232 2.0 15.3 1.0 OH5 B:XYH404 2.0 16.0 0.5 ON B:LLH405 2.0 13.9 0.5 OD1 B:ASP206 2.0 17.8 1.0 OE1 B:GLU258 2.0 14.5 1.0 O B:HOH786 2.1 16.0 1.0 O1 B:LLH405 2.1 16.4 0.5 OH6 B:XYH404 2.5 17.1 0.5 N B:LLH405 2.7 15.0 0.5 C1 B:LLH405 2.7 16.9 0.5 C5 B:XYH404 3.0 17.1 0.5 CD B:GLU258 3.0 18.2 1.0 CD B:GLU232 3.1 17.8 1.0 CG B:ASP206 3.1 16.2 1.0 N6 B:XYH404 3.1 13.6 0.5 OE2 B:GLU258 3.4 16.6 1.0 OD2 B:ASP206 3.5 16.2 1.0 CG B:GLU232 3.8 12.3 1.0 NH1 B:ARG280 3.9 14.5 1.0 NZ B:LYS169 3.9 14.0 1.0 OE1 B:GLU232 4.0 15.8 1.0 NE B:ARG280 4.0 13.7 1.0 OH2 B:XYH404 4.0 30.1 0.5 NE2 B:HIS171 4.1 17.4 1.0 C2 B:LLH405 4.2 21.4 0.5 O4 B:LLH405 4.3 29.7 0.5 CB B:ASP206 4.3 13.3 1.0 CG B:GLU258 4.3 14.9 1.0 NH1 A:ARG90 4.4 21.7 1.0 CZ B:ARG280 4.4 15.3 1.0 C4 B:XYH404 4.4 22.4 0.5 OE2 B:GLU233 4.4 17.5 1.0 CB B:GLU258 4.6 13.6 1.0 O3 B:LLH405 4.6 23.0 0.5 CE B:LYS169 4.7 14.1 1.0 CD2 B:HIS309 4.7 19.0 1.0 OH4 B:XYH404 4.8 22.0 0.5 CD2 B:HIS171 4.8 19.2 1.0 C3 B:LLH405 4.9 24.9 0.5 CE1 B:HIS209 5.0 14.8 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:14.4 occ:0.96 O B:LEU250 2.0 16.2 1.0 O B:HOH790 2.1 15.0 1.0 O B:HOH789 2.1 15.9 1.0 O B:SER247 2.1 16.0 1.0 O B:HOH787 2.1 16.1 1.0 O B:HOH788 2.1 19.6 1.0 C B:LEU250 3.2 15.4 1.0 C B:SER247 3.2 16.4 1.0 CA B:SER247 3.9 15.3 1.0 OD2 B:ASP277 4.1 14.9 1.0 CA B:LEU250 4.2 14.2 1.0 N B:ASP251 4.2 14.8 1.0 N B:LEU250 4.2 14.2 1.0 O B:HOH679 4.2 39.1 1.0 O B:HOH642 4.2 27.1 1.0 CA B:ASP251 4.2 17.9 1.0 OD1 B:ASP277 4.3 17.0 1.0 O B:ASP251 4.3 17.9 1.0 N B:ASP248 4.3 14.1 1.0 C B:ASP251 4.4 16.3 1.0 O B:ILE252 4.4 14.2 1.0 C B:ASP248 4.5 19.2 1.0 CB B:SER247 4.5 18.8 1.0 CB B:LEU250 4.5 13.8 1.0 CA B:ASP248 4.5 14.7 1.0 CG B:ASP277 4.6 16.9 1.0 O B:ASP248 4.6 18.8 1.0 O B:HOH858 4.8 29.0 1.0 C B:ASN249 4.9 21.1 1.0 N B:ASN249 4.9 13.6 1.0 O B:LEU246 4.9 13.6 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, L-Xylarohydroxamate and L-Lyxarohydroxamate To Be Published.