Magnesium in PDB 4r74: Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound)

The structure of Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound), PDB code: 4r74 was solved by B.Sit, C.Calmettes, T.F.Moraes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.49 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.202, 96.988, 145.075, 90.00, 95.93, 90.00
R / Rfree (%)	15.1 / 20.2

The binding sites of Magnesium atom in the Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound) (pdb code 4r74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound), PDB code: 4r74:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg408 b:10.1 occ:1.00 O A:HOH530 3.1 15.4 1.0 O A:HOH510 3.1 12.1 1.0 O2 A:GOL405 3.1 39.1 0.8 O A:HOH750 3.1 16.3 1.0 N B:ASN244 3.3 11.9 1.0 CA B:ASN241 3.6 14.2 1.0 ND2 B:ASN244 3.7 11.1 1.0 CG B:ASN244 3.7 13.1 1.0 C B:ASN241 3.7 14.3 1.0 C1 A:GOL405 3.7 23.9 0.8 N B:ASP243 3.8 12.0 1.0 CB B:ASP243 3.8 11.3 1.0 CB B:ASN241 3.8 12.0 1.0 CB B:ASN244 3.9 10.9 1.0 O B:ASN241 3.9 14.9 1.0 C2 A:GOL405 4.0 32.0 0.8 CA B:ASP243 4.1 13.3 1.0 C B:ASP243 4.1 11.7 1.0 OD1 B:ASN244 4.2 11.6 1.0 CA B:ASN244 4.2 11.8 1.0 N B:LEU242 4.2 11.7 1.0 OD1 B:ASN241 4.5 18.4 1.0 O3 A:GOL405 4.5 25.7 0.8 CG B:ASP243 4.6 14.6 1.0 OD2 B:ASP243 4.6 11.6 1.0 OG1 A:THR187 4.6 11.3 1.0 C3 A:GOL405 4.6 25.0 0.8 O B:ARG3 4.7 12.4 1.0 CG B:ASN241 4.7 19.3 1.0 C B:LEU242 4.7 13.4 1.0 NH1 A:ARG190 4.7 17.5 1.0 O1 A:GOL405 4.8 37.0 0.8 O B:HOH570 4.8 22.0 1.0 OG A:SER184 4.9 22.2 1.0 O B:ARG240 5.0 21.8 1.0 N B:ASN241 5.0 13.5 1.0

Magnesium binding site 2 out of 3 in the Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg406 b:13.6 occ:1.00 OD2 D:ASP82 1.9 33.5 1.0 CG D:ASP82 2.9 28.7 1.0 OD1 D:ASP82 3.2 26.6 1.0 CB D:ASP82 4.3 22.0 1.0 NH1 D:ARG77 4.5 26.4 1.0 O D:PRO79 4.6 23.6 1.0

Magnesium binding site 3 out of 3 in the Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Periplasmic Binding Protein Afua From Actinobacillus Pleuropneumoniae (Exogenous Fructose-6-Phosphate Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg407 b:16.3 occ:1.00 O B:HOH739 3.0 22.8 1.0 O2 B:GOL402 3.2 36.3 1.0 N D:ASN244 3.2 17.4 1.0 O B:HOH513 3.3 12.0 1.0 O B:HOH536 3.3 15.5 1.0 ND2 D:ASN244 3.4 22.9 1.0 CG D:ASN244 3.5 18.9 1.0 CB D:ASN244 3.7 20.9 1.0 CB D:ASP243 3.7 18.9 1.0 N D:ASP243 3.7 16.7 1.0 C D:ASN241 3.8 19.5 1.0 CA D:ASN241 3.9 18.4 1.0 O D:ASN241 3.9 23.3 1.0 CB D:ASN241 4.0 20.1 1.0 CA D:ASP243 4.0 16.3 1.0 C D:ASP243 4.0 15.5 1.0 OD1 D:ASN244 4.0 17.7 1.0 CA D:ASN244 4.0 21.9 1.0 O3 B:GOL402 4.3 25.8 1.0 N D:LEU242 4.4 18.4 1.0 C2 B:GOL402 4.4 29.1 1.0 C3 B:GOL402 4.5 37.2 1.0 OD1 D:ASN241 4.6 27.5 1.0 CG D:ASP243 4.6 14.3 1.0 OD2 D:ASP243 4.6 11.0 1.0 C D:LEU242 4.7 13.3 1.0 O D:ARG3 4.7 18.2 1.0 OG1 B:THR187 4.8 13.8 1.0 CG D:ASN241 4.8 28.9 1.0 NH1 B:ARG190 4.8 13.4 1.0 OG B:SER184 4.9 22.3 1.0

B.Sit, S.M.Crowley, K.Bhullar, C.C.Lai, C.Tang, Y.Hooda, C.Calmettes, H.Khambati, C.Ma, J.H.Brumell, A.B.Schryvers, B.A.Vallance, T.F.Moraes. Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of A Bacterial Pathogen. Plos Pathog. V. 11 05107 2015.
ISSN: ISSN 1553-7366
PubMed: 26295949
DOI: 10.1371/JOURNAL.PPAT.1005107