Magnesium in PDB 3p0w: Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate

The structure of Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate, PDB code: 3p0w was solved by A.A.Fedorov, E.V.Fedorov, J.A.Gerlt, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.958, 128.822, 178.100, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate (pdb code 3p0w). 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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate, PDB code: 3p0w:
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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg471 b:40.2 occ:1.00 O A:HOH512 2.1 33.7 1.0 OE2 A:GLU276 2.2 37.4 1.0 OD1 A:ASN305 2.2 43.4 1.0 OD2 A:ASP251 2.3 34.6 1.0 O6B A:GKR472 2.4 42.6 1.0 O6A A:GKR472 2.4 46.2 1.0 C6 A:GKR472 2.7 48.4 1.0 CG A:ASN305 2.9 39.6 1.0 ND2 A:ASN305 2.9 39.8 1.0 CG A:ASP251 3.1 35.5 1.0 CD A:GLU276 3.2 35.4 1.0 OD1 A:ASP251 3.3 33.2 1.0 CG A:GLU276 3.6 36.1 1.0 OD2 A:ASP277 3.9 32.7 1.0 NZ A:LYS221 4.2 42.2 1.0 C5 A:GKR472 4.2 50.6 1.0 OE1 A:GLU276 4.2 39.7 1.0 CB A:ASN305 4.4 33.9 1.0 ND2 A:ASN253 4.4 43.6 1.0 CB A:ASP251 4.5 35.4 1.0 N A:ASN305 4.7 33.2 1.0 NZ A:LYS223 4.7 42.6 1.0 CG A:ASN253 4.9 44.1 1.0 O5 A:GKR472 4.9 47.0 1.0 CG A:ASP277 4.9 33.4 1.0 OD1 A:ASN253 4.9 46.5 1.0 OH A:TYR166 4.9 47.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg471 b:38.8 occ:1.00 O B:HOH563 2.1 27.5 1.0 OE2 B:GLU276 2.1 30.5 1.0 OD1 B:ASN305 2.2 34.8 1.0 O6B B:GKR472 2.3 36.3 1.0 OD2 B:ASP251 2.4 31.6 1.0 O6A B:GKR472 2.4 35.4 1.0 C6 B:GKR472 2.6 38.5 1.0 CD B:GLU276 3.0 30.4 1.0 CG B:ASP251 3.0 33.0 1.0 CG B:ASN305 3.2 34.2 1.0 OD1 B:ASP251 3.3 33.6 1.0 CG B:GLU276 3.4 32.8 1.0 ND2 B:ASN305 3.5 32.4 1.0 NZ B:LYS221 3.7 38.3 1.0 OE1 B:GLU276 4.1 37.1 1.0 ND2 B:ASN253 4.1 40.7 1.0 C5 B:GKR472 4.1 41.6 1.0 OD2 B:ASP277 4.1 31.2 1.0 CB B:ASP251 4.2 34.8 1.0 NZ B:LYS223 4.2 41.0 1.0 CE B:LYS221 4.5 36.5 1.0 CB B:ASN305 4.5 32.8 1.0 CD1 B:LEU327 4.7 35.2 1.0 N B:ASN305 4.8 26.6 1.0 CB B:GLU276 4.8 32.5 1.0 O5 B:GKR472 4.8 41.3 1.0 CD2 B:HIS355 4.9 36.2 1.0 CG B:ASN253 4.9 42.2 1.0 OH B:TYR166 5.0 40.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg471 b:43.7 occ:1.00 O C:HOH513 2.1 37.5 1.0 OD2 C:ASP251 2.2 37.1 1.0 OD1 C:ASN305 2.2 45.1 1.0 OE2 C:GLU276 2.3 40.1 1.0 O6A C:GKR472 2.4 49.1 1.0 O6B C:GKR472 2.4 43.5 1.0 C6 C:GKR472 2.7 49.5 1.0 CG C:ASN305 3.0 37.9 1.0 CG C:ASP251 3.0 36.8 1.0 ND2 C:ASN305 3.2 40.0 1.0 CD C:GLU276 3.3 38.7 1.0 OD1 C:ASP251 3.3 36.0 1.0 OD2 C:ASP277 3.6 31.9 1.0 CG C:GLU276 3.7 35.6 1.0 ND2 C:ASN253 3.9 44.5 1.0 NZ C:LYS221 4.1 42.9 1.0 NZ C:LYS223 4.2 45.1 1.0 C5 C:GKR472 4.2 49.7 1.0 CB C:ASP251 4.3 35.6 1.0 CB C:ASN305 4.4 35.5 1.0 OE1 C:GLU276 4.4 41.1 1.0 CG C:ASP277 4.6 34.7 1.0 N C:ASN305 4.6 35.4 1.0 CG C:ASN253 4.7 43.9 1.0 CB C:ASP277 4.8 38.1 1.0 CE C:LYS221 4.9 44.3 1.0 C4 C:GKR472 5.0 47.9 1.0 CG C:MET306 5.0 36.1 1.0 O5 C:GKR472 5.0 45.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg471 b:45.3 occ:1.00 OD1 D:ASN305 2.2 39.2 1.0 O D:HOH509 2.2 41.9 1.0 OE2 D:GLU276 2.2 44.7 1.0 OD2 D:ASP251 2.3 40.6 1.0 O6B D:GKR472 2.4 43.8 1.0 O6A D:GKR472 2.5 48.4 1.0 C6 D:GKR472 2.8 50.3 1.0 CG D:ASP251 3.0 37.8 1.0 OD1 D:ASP251 3.1 35.2 1.0 CD D:GLU276 3.2 34.9 1.0 CG D:ASN305 3.2 41.8 1.0 CG D:GLU276 3.7 36.7 1.0 OD2 D:ASP277 3.8 35.3 1.0 ND2 D:ASN305 3.9 42.3 1.0 O D:HOH504 4.0 45.0 1.0 OE1 D:GLU276 4.2 42.3 1.0 NZ D:LYS223 4.2 46.7 1.0 C5 D:GKR472 4.3 51.7 1.0 CB D:ASP251 4.3 40.4 1.0 CB D:ASN305 4.4 40.3 1.0 OD1 D:ASN253 4.5 45.3 1.0 N D:ASN305 4.6 39.6 1.0 CG D:ASN253 4.8 46.2 1.0 CG D:MET306 4.9 42.4 1.0 CG D:ASP277 4.9 38.4 1.0 ND2 D:ASN253 4.9 44.6 1.0 CB D:GLU276 4.9 36.7 1.0 CA D:ASN305 5.0 39.3 1.0

A.A.Fedorov, E.V.Fedorov, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate To Be Published.