Magnesium in PDB 7smg: Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae

The structure of Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae, PDB code: 7smg was solved by S.Ahmad, A.G.Alexei, K.K.Tsang, S.Trilesky, Y.Kim, J.C.Whitney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.64 / 2.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	144.136, 144.136, 63.485, 90, 90, 120
R / Rfree (%)	20.1 / 23.5

The structure of Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae (pdb code 7smg). 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 A (P)Ppapp Hydrolase From Bacteroides Caccae, PDB code: 7smg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae


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 A (P)Ppapp Hydrolase From Bacteroides Caccae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:33.0 occ:1.00 OD1 A:ASP110 2.1 45.8 1.0 O A:HOH303 2.1 49.4 1.0 O A:HOH316 2.1 43.9 1.0 NE2 A:HIS53 2.2 49.9 1.0 OD2 A:ASP54 2.3 50.0 1.0 NE2 A:HIS33 2.3 48.1 1.0 CD2 A:HIS53 2.8 43.5 1.0 CG A:ASP110 3.1 48.2 1.0 CG A:ASP54 3.1 52.5 1.0 CD2 A:HIS33 3.3 48.9 1.0 CE1 A:HIS33 3.3 47.0 1.0 CE1 A:HIS53 3.4 45.9 1.0 OD1 A:ASP54 3.4 55.9 1.0 OD2 A:ASP110 3.7 53.1 1.0 OH A:TYR30 4.0 51.2 1.0 CG A:HIS53 4.1 44.9 1.0 CB A:ASP110 4.2 45.5 1.0 ND1 A:HIS53 4.3 45.1 1.0 ND2 A:ASN114 4.4 54.5 1.0 ND1 A:HIS33 4.4 45.5 1.0 CG A:HIS33 4.4 48.5 1.0 O A:HOH313 4.4 47.9 1.0 CB A:ASP54 4.5 51.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae


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 A (P)Ppapp Hydrolase From Bacteroides Caccae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:35.8 occ:1.00 O B:HOH332 2.1 57.2 1.0 OD1 B:ASP110 2.1 41.6 1.0 NE2 B:HIS53 2.1 44.1 1.0 O B:HOH321 2.2 46.0 1.0 NE2 B:HIS33 2.3 41.7 1.0 OD2 B:ASP54 2.8 74.7 1.0 CD2 B:HIS53 3.0 43.5 1.0 CG B:ASP110 3.0 40.9 1.0 CE1 B:HIS53 3.2 40.1 1.0 CD2 B:HIS33 3.3 40.5 1.0 CE1 B:HIS33 3.3 42.1 1.0 OD2 B:ASP110 3.4 45.0 1.0 OH B:TYR30 3.9 53.6 1.0 CG B:ASP54 4.0 66.2 1.0 CG B:HIS53 4.2 38.8 1.0 ND1 B:HIS53 4.3 37.0 1.0 CB B:ASP110 4.3 41.5 1.0 ND2 B:ASN114 4.4 49.1 1.0 CG B:HIS33 4.4 41.0 1.0 ND1 B:HIS33 4.4 40.2 1.0 CB B:ASP54 4.7 51.3 1.0 OD1 B:ASN114 4.8 48.2 1.0 OD1 B:ASP54 4.9 65.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae


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 A (P)Ppapp Hydrolase From Bacteroides Caccae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:33.4 occ:1.00 O C:HOH314 2.0 49.0 1.0 OD1 C:ASP110 2.1 46.7 1.0 NE2 C:HIS53 2.2 48.8 1.0 O C:HOH320 2.2 54.0 1.0 NE2 C:HIS33 2.3 49.0 1.0 OD1 C:ASP54 2.4 59.5 1.0 CG C:ASP110 2.9 45.5 1.0 CD2 C:HIS53 3.0 47.3 1.0 CD2 C:HIS33 3.2 45.9 1.0 OD2 C:ASP110 3.2 47.3 1.0 CE1 C:HIS53 3.2 47.5 1.0 CE1 C:HIS33 3.3 45.9 1.0 CG C:ASP54 3.5 63.7 1.0 OD2 C:ASP54 4.0 70.8 1.0 OH C:TYR30 4.2 59.8 1.0 CG C:HIS53 4.2 46.7 1.0 CB C:ASP110 4.3 40.4 1.0 ND1 C:HIS53 4.3 51.7 1.0 ND1 C:HIS33 4.4 43.8 1.0 CG C:HIS33 4.4 43.9 1.0 ND2 C:ASN114 4.6 49.2 1.0 CB C:ASP54 4.8 55.9 1.0 OD1 C:ASN114 4.8 49.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae


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 A (P)Ppapp Hydrolase From Bacteroides Caccae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:35.3 occ:1.00 OD1 D:ASP110 2.0 46.1 1.0 O D:HOH311 2.2 49.1 1.0 NE2 D:HIS53 2.2 49.6 1.0 NE2 D:HIS33 2.3 47.6 1.0 O D:HOH318 2.4 59.4 1.0 OD2 D:ASP54 2.5 62.0 1.0 CG D:ASP110 3.1 44.7 1.0 CD2 D:HIS53 3.2 46.6 1.0 CD2 D:HIS33 3.2 49.2 1.0 CE1 D:HIS53 3.2 47.9 1.0 CE1 D:HIS33 3.3 44.0 1.0 CG D:ASP54 3.6 70.9 1.0 OD2 D:ASP110 3.6 46.6 1.0 OD1 D:ASP54 4.1 76.8 1.0 OH D:TYR30 4.2 61.4 1.0 CB D:ASP110 4.2 42.6 1.0 CG D:HIS53 4.3 44.8 1.0 ND1 D:HIS53 4.3 44.8 1.0 ND2 D:ASN114 4.4 51.3 1.0 ND1 D:HIS33 4.4 44.9 1.0 CG D:HIS33 4.4 48.0 1.0 CB D:ASP54 4.8 65.1 1.0 OD1 D:ASN114 4.9 51.5 1.0

S.Ahmad, A.G.Alexei, K.K.Tsang, S.Trilesky, Y.Kim, J.C.Whitney. Crystal Structure of A (P)Ppapp Hydrolase From Bacteroides Caccae To Be Published.