Magnesium in PDB 3pfr: Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate

The structure of Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate, PDB code: 3pfr was solved by A.A.Fedorov, E.V.Fedorov, F.Mills-Groninger, S.Ghasempur, 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)	38.86 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	85.712, 85.712, 253.238, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.3

The binding sites of Magnesium atom in the Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate (pdb code 3pfr). 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 Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate, PDB code: 3pfr:
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 Related Protein From Actinobacillus Succinogenes Complexed with 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 Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg456 b:29.5 occ:1.00 O A:HOH801 2.1 23.6 1.0 OD1 A:ASN290 2.1 25.6 1.0 OE2 A:GLU261 2.1 24.8 1.0 O6A A:GKR457 2.2 28.7 1.0 OD1 A:ASP236 2.3 28.1 1.0 O6B A:GKR457 2.4 26.3 1.0 C6 A:GKR457 2.6 26.8 1.0 CG A:ASN290 3.1 24.6 1.0 CG A:ASP236 3.1 26.8 1.0 CD A:GLU261 3.2 25.1 1.0 ND2 A:ASN290 3.4 27.3 1.0 OD2 A:ASP236 3.5 25.0 1.0 CG A:GLU261 3.7 24.5 1.0 NZ A:LYS206 3.8 29.6 1.0 ND2 A:ASN238 3.9 27.9 1.0 OD2 A:ASP262 4.0 24.5 1.0 C5 A:GKR457 4.1 29.9 1.0 NZ A:LYS208 4.2 26.6 1.0 OE1 A:GLU261 4.3 24.2 1.0 CB A:ASP236 4.3 27.9 1.0 CB A:ASN290 4.5 25.2 1.0 CE A:LYS206 4.6 26.4 1.0 CD2 A:HIS340 4.6 27.6 0.5 CG A:ASN238 4.7 29.8 1.0 N A:ASN290 4.9 24.3 1.0 O5 A:GKR457 4.9 28.6 1.0 OH A:TYR151 4.9 28.0 1.0 C4 A:GKR457 4.9 28.1 1.0 CB A:GLU261 4.9 24.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with 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 Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg456 b:30.0 occ:1.00 O B:HOH802 2.1 23.6 1.0 OD1 B:ASN290 2.1 25.7 1.0 OE2 B:GLU261 2.1 23.7 1.0 O6A B:GKR457 2.2 28.6 1.0 O6B B:GKR457 2.4 26.4 1.0 OD1 B:ASP236 2.4 27.1 1.0 C6 B:GKR457 2.7 26.4 1.0 CG B:ASN290 3.0 24.0 1.0 CG B:ASP236 3.2 27.0 1.0 ND2 B:ASN290 3.2 23.9 1.0 CD B:GLU261 3.2 24.6 1.0 OD2 B:ASP236 3.5 24.4 1.0 CG B:GLU261 3.7 24.1 1.0 ND2 B:ASN238 3.9 27.4 1.0 NZ B:LYS206 3.9 28.2 1.0 OD2 B:ASP262 4.0 22.2 1.0 C5 B:GKR457 4.2 28.9 1.0 OE1 B:GLU261 4.3 26.6 1.0 NZ B:LYS208 4.3 26.1 1.0 CB B:ASP236 4.4 25.2 1.0 CB B:ASN290 4.4 25.0 1.0 CD2 B:HIS340 4.6 26.6 0.5 N B:ASN290 4.7 24.5 1.0 CG B:ASN238 4.7 30.1 1.0 CE B:LYS206 4.8 28.2 1.0 O B:HOH806 4.9 30.7 1.0 CB B:GLU261 4.9 22.7 1.0 CD1 B:LEU312 4.9 26.0 1.0 CG B:ASP262 5.0 26.4 1.0 O5 B:GKR457 5.0 29.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with 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 Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg456 b:28.4 occ:1.00 OE2 C:GLU261 2.1 24.9 1.0 OD1 C:ASN290 2.2 26.9 1.0 OD1 C:ASP236 2.2 27.7 1.0 O6B C:GKR457 2.3 26.9 1.0 O C:HOH803 2.4 27.5 1.0 O6A C:GKR457 2.5 32.0 1.0 C6 C:GKR457 2.8 29.1 1.0 CG C:ASP236 2.9 26.7 1.0 CD C:GLU261 3.1 25.1 1.0 CG C:ASN290 3.1 26.6 1.0 OD2 C:ASP236 3.3 25.9 1.0 CG C:GLU261 3.5 24.7 1.0 ND2 C:ASN290 3.5 24.7 1.0 NZ C:LYS206 3.6 27.3 1.0 CB C:ASP236 4.1 26.1 1.0 OE1 C:GLU261 4.2 27.4 1.0 OD2 C:ASP262 4.2 27.7 1.0 ND2 C:ASN238 4.2 28.1 1.0 NZ C:LYS208 4.2 28.1 1.0 C5 C:GKR457 4.3 29.2 1.0 CE C:LYS206 4.5 29.6 1.0 CB C:ASN290 4.5 24.5 1.0 CD1 C:LEU312 4.6 25.6 1.0 CB C:GLU261 4.7 28.3 1.0 N C:ASN290 4.8 24.9 1.0 CD2 C:HIS340 4.9 27.1 0.4 OH C:TYR151 4.9 28.9 1.0 CG C:ASN238 5.0 29.8 1.0 O5 C:GKR457 5.0 29.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with 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 Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg456 b:27.9 occ:1.00 OE2 D:GLU261 2.1 23.6 1.0 OD1 D:ASN290 2.2 25.4 1.0 OD1 D:ASP236 2.2 28.0 1.0 O D:HOH808 2.2 27.5 1.0 O6B D:GKR457 2.3 25.8 1.0 O6A D:GKR457 2.4 29.0 1.0 C6 D:GKR457 2.7 27.8 1.0 CG D:ASP236 3.0 26.9 1.0 CG D:ASN290 3.1 25.8 1.0 CD D:GLU261 3.2 25.7 1.0 ND2 D:ASN290 3.3 25.2 1.0 OD2 D:ASP236 3.3 26.4 1.0 CG D:GLU261 3.6 24.9 1.0 NZ D:LYS206 3.8 28.5 1.0 NZ D:LYS208 4.0 28.6 1.0 OD2 D:ASP262 4.1 27.2 1.0 ND2 D:ASN238 4.1 28.3 1.0 CB D:ASP236 4.2 26.6 1.0 C5 D:GKR457 4.2 28.9 1.0 OE1 D:GLU261 4.2 27.0 1.0 CB D:ASN290 4.5 25.4 1.0 CE D:LYS206 4.6 28.1 1.0 CD1 D:LEU312 4.7 25.9 1.0 N D:ASN290 4.7 25.0 1.0 CD2 D:HIS340 4.9 27.0 0.4 CB D:GLU261 4.9 27.7 1.0 CG D:ASN238 4.9 29.4 1.0 OH D:TYR151 4.9 29.9 1.0 O5 D:GKR457 4.9 30.2 1.0

A.A.Fedorov, E.V.Fedorov, F.Mills-Groninger, S.Ghasempur, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Glucarate Dehydratase Related Protein From Actinobacillus Succinogenes Complexed with D-Glucarate To Be Published.