Magnesium 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:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

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

Magnesium binding site 1 out of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:5.4 occ:1.00 OE2 A:GLU232 2.0 8.7 1.0 OE1 A:GLU258 2.0 6.0 1.0 OD1 A:ASP206 2.0 8.0 1.0 O A:HOH966 2.0 6.4 1.0 O A:HOH964 2.2 8.8 1.0 O A:HOH963 2.2 8.7 1.0 CD A:GLU258 3.0 9.4 1.0 CG A:ASP206 3.1 7.5 1.0 CD A:GLU232 3.1 7.2 1.0 OE2 A:GLU258 3.3 7.3 1.0 OD2 A:ASP206 3.6 7.0 1.0 CG A:GLU232 3.8 4.2 1.0 NH1 A:ARG280 4.0 5.0 1.0 OE1 A:GLU232 4.1 7.1 1.0 NZ A:LYS169 4.1 5.1 1.0 NE2 A:HIS171 4.1 7.0 1.0 NE A:ARG280 4.2 4.5 1.0 CB A:ASP206 4.3 6.3 1.0 CG A:GLU258 4.3 7.0 1.0 O A:HOH637 4.3 12.3 1.0 OE2 A:GLU233 4.4 6.9 1.0 CB A:GLU258 4.5 6.3 1.0 CZ A:ARG280 4.6 5.2 1.0 CD2 A:HIS309 4.6 7.7 1.0 O A:HOH581 4.6 15.9 1.0 CD2 A:HIS171 4.7 10.9 1.0 CE1 A:HIS209 4.7 5.8 1.0 CE A:LYS169 4.9 4.2 1.0 NE2 A:HIS309 4.9 9.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:7.1 occ:1.00 O A:LEU250 2.1 10.5 1.0 O A:SER247 2.2 8.0 0.6 O A:SER247 2.2 8.0 0.4 O A:HOH972 2.2 12.7 1.0 O A:HOH514 2.3 8.3 1.0 O A:HOH786 2.3 13.2 1.0 O A:HOH721 2.3 18.6 1.0 C A:LEU250 3.3 7.6 1.0 C A:SER247 3.3 7.6 0.6 C A:SER247 3.3 7.6 0.4 CA A:SER247 4.0 6.1 0.6 CA A:SER247 4.0 6.2 0.4 O A:HOH1012 4.0 30.2 1.0 O A:HOH551 4.1 12.6 1.0 N A:LEU250 4.1 6.8 1.0 CA A:LEU250 4.2 6.0 1.0 N A:ASP251 4.2 9.6 1.0 OD2 A:ASP277 4.2 5.7 1.0 CA A:ASP251 4.3 11.6 1.0 N A:ASP248 4.4 7.6 1.0 O A:ASP251 4.4 11.6 1.0 OD1 A:ASP277 4.4 7.7 1.0 C A:ASP251 4.4 9.2 1.0 CB A:SER247 4.5 9.2 0.6 O A:ILE252 4.5 6.5 1.0 CB A:LEU250 4.5 5.5 1.0 CB A:SER247 4.6 9.3 0.4 CA A:ASP248 4.7 9.4 1.0 C A:ASP248 4.7 13.7 1.0 CG A:ASP277 4.7 6.7 1.0 O A:ASP248 4.9 17.0 1.0 N A:ASN249 5.0 6.5 1.0 O A:LEU246 5.0 5.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:25.0 occ:1.00 O A:LEU346 2.1 15.7 1.0 O A:HOH994 2.2 31.5 1.0 O A:HIS343 2.3 10.5 1.0 O A:HOH752 2.5 25.3 1.0 O A:HOH973 2.7 13.2 1.0 C A:LEU346 3.3 9.7 1.0 C A:HIS343 3.4 10.3 1.0 N A:HIS343 3.8 12.1 1.0 O A:HOH877 3.8 40.8 1.0 O A:HOH661 4.1 15.0 1.0 N A:LEU346 4.2 8.5 1.0 O A:HOH953 4.2 27.7 1.0 CA A:LEU346 4.2 8.2 1.0 N A:ASP344 4.2 10.5 1.0 CA A:HIS343 4.2 13.4 1.0 N A:LYS347 4.2 12.1 1.0 O A:ASP341 4.3 20.5 1.0 CA A:ASP344 4.3 14.0 1.0 O A:HOH582 4.3 12.9 1.0 C A:LYS347 4.3 13.6 1.0 CA A:LYS347 4.3 9.6 1.0 C A:ASP344 4.4 13.7 1.0 O A:LYS347 4.5 13.7 1.0 C A:GLY342 4.5 13.1 1.0 CB A:LEU346 4.6 11.2 1.0 O A:ASP344 4.6 14.6 1.0 N A:SER348 4.6 9.1 0.7 N A:SER348 4.7 9.2 0.3 O A:HOH812 4.8 19.4 1.0 CA A:GLY342 4.9 13.6 1.0 N A:TYR345 5.0 11.0 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.