Magnesium in PDB 1xz8: Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form

All present enzymatic activity of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form:
2.4.2.9;

The structure of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form, PDB code: 1xz8 was solved by P.Chander, K.M.Halbig, J.K.Miller, C.J.Fields, H.K.Bonner, G.K.Grabner, R.L.Switzer, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	128.540, 128.540, 128.760, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 30

The binding sites of Magnesium atom in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form (pdb code 1xz8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form, PDB code: 1xz8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg180 b:43.4 occ:1.00 O A:HOH323 2.0 21.6 1.0 O A:HOH324 2.0 28.1 1.0 OD1 A:ASP105 2.0 35.2 1.0 OD2 A:ASP104 2.0 36.8 1.0 O1P A:3GP300 2.1 47.6 1.0 O A:HOH322 2.7 39.5 1.0 CG A:ASP104 2.9 34.9 1.0 CG A:ASP105 3.2 33.8 1.0 OD1 A:ASP104 3.2 37.1 1.0 P A:3GP300 3.4 46.8 1.0 O3' A:5GP200 3.4 58.6 1.0 O3P A:3GP300 3.5 48.0 1.0 N A:VAL106 3.8 28.5 1.0 N A:ASP105 3.8 30.0 1.0 OD2 A:ASP105 3.9 35.0 1.0 C3' A:5GP200 3.9 55.8 1.0 O2P A:3GP300 4.0 49.4 1.0 O A:VAL106 4.2 27.5 1.0 CB A:ASP105 4.3 33.1 1.0 CB A:ASP104 4.3 32.9 1.0 CA A:ASP105 4.4 30.8 1.0 O A:ILE38 4.6 30.6 1.0 C2' A:5GP200 4.6 53.9 1.0 C A:ASP105 4.6 29.5 1.0 C A:ASP104 4.6 29.8 1.0 CA A:VAL106 4.7 28.1 1.0 O A:HOH317 4.7 44.0 1.0 CA A:ASP104 4.7 30.7 1.0 O3' A:3GP300 4.7 49.8 1.0 C A:VAL106 4.9 27.8 1.0 CB A:VAL106 4.9 26.0 1.0 N3 A:5GP200 4.9 45.5 1.0

Magnesium binding site 2 out of 2 in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg180 b:43.2 occ:1.00 O B:HOH424 1.7 44.1 1.0 O3' B:U5P400 1.9 75.0 1.0 OD1 B:ASP105 2.0 27.8 1.0 OD2 B:ASP104 2.3 36.7 1.0 O B:HOH425 2.5 40.7 1.0 CG B:ASP104 2.9 30.3 1.0 OD1 B:ASP104 2.9 29.0 1.0 CG B:ASP105 3.3 26.8 1.0 C3' B:U5P400 3.3 76.3 1.0 O2' B:U5P400 3.4 75.7 1.0 O B:ILE38 3.6 35.0 1.0 N B:ASP105 3.7 24.3 1.0 C2' B:U5P400 3.8 77.2 1.0 OD2 B:ASP105 3.9 27.3 1.0 CB B:ASP104 4.2 27.7 1.0 N B:VAL106 4.3 23.9 1.0 C4' B:U5P400 4.3 74.7 1.0 CB B:ASP105 4.4 25.9 1.0 CA B:ASP104 4.4 24.9 1.0 CA B:ASP105 4.5 25.0 1.0 CG B:LYS39 4.5 43.5 1.0 C B:ASP104 4.5 24.9 1.0 CB B:LYS39 4.5 39.9 1.0 O B:HOH404 4.7 22.8 1.0 C B:ILE38 4.7 34.1 1.0 O B:VAL106 4.8 27.4 1.0 CG2 B:ILE38 4.8 34.8 1.0 N B:GLY42 4.9 39.7 1.0 C B:ASP105 4.9 25.3 1.0 CB B:ILE38 5.0 33.1 1.0

P.Chander, K.M.Halbig, J.K.Miller, C.J.Fields, H.K.Bonner, G.K.Grabner, R.L.Switzer, J.L.Smith. Structure of the Nucleotide Complex of Pyrr, the Pyr Attenuation Protein From Bacillus Caldolyticus, Suggests Dual Regulation By Pyrimidine and Purine Nucleotides. J.Bacteriol. V. 187 1773 2005.
ISSN: ISSN 0021-9193
PubMed: 15716449
DOI: 10.1128/JB.187.5.1773-1782.2005