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

Enzymatic activity of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Sulfate-Bound Form

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

Protein crystallography data

The structure of Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Sulfate-Bound Form, PDB code: 1xzn 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 / 2.27
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.460, 106.460, 62.200, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Sulfate-Bound Form (pdb code 1xzn). 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, Sulfate-Bound Form, PDB code: 1xzn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1xzn

Go back to Magnesium Binding Sites List in 1xzn
Magnesium binding site 1 out of 2 in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Sulfate-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, Sulfate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg200

b:31.1
occ:1.00
OD1 A:ASP105 2.1 39.0 1.0
O A:HOH318 2.1 43.9 1.0
OD2 A:ASP104 2.2 35.0 1.0
O A:HOH305 2.3 43.0 1.0
O A:HOH306 2.4 56.0 1.0
CG A:ASP104 3.2 35.4 1.0
CG A:ASP105 3.2 39.9 1.0
OD1 A:ASP104 3.5 31.5 1.0
OD2 A:ASP105 3.8 42.3 1.0
N A:ASP105 3.8 36.3 1.0
N A:VAL106 4.2 34.0 1.0
CB A:ASP105 4.3 38.2 1.0
O A:ILE38 4.4 40.9 1.0
O3 A:SO4303 4.4 83.7 1.0
CB A:ASP104 4.4 32.4 1.0
CD A:LYS39 4.5 54.4 1.0
O4 A:SO4303 4.5 83.7 1.0
CA A:ASP105 4.5 36.4 1.0
CA A:ASP104 4.7 35.4 1.0
O A:VAL106 4.7 33.0 1.0
C A:ASP104 4.7 36.0 1.0
NZ A:LYS39 4.9 56.3 1.0
C A:ASP105 4.9 35.1 1.0
CB A:LYS39 5.0 46.8 1.0

Magnesium binding site 2 out of 2 in 1xzn

Go back to Magnesium Binding Sites List in 1xzn
Magnesium binding site 2 out of 2 in the Pyrr, the Regulator of the Pyrimidine Biosynthetic Operon in Bacillus Caldolyticus, Sulfate-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, Sulfate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:44.8
occ:0.50
O B:HOH328 2.3 54.2 1.0
OD1 B:ASP105 2.3 45.8 1.0
OD2 B:ASP104 2.4 47.1 1.0
O B:HOH333 2.9 48.4 1.0
CG B:ASP104 3.3 48.1 1.0
CG B:ASP105 3.4 46.0 1.0
OD1 B:ASP104 3.5 49.9 1.0
CD B:LYS39 3.5 20.0 1.0
OD2 B:ASP105 3.9 46.7 1.0
O B:ILE38 4.0 51.5 1.0
CB B:LYS39 4.0 55.2 1.0
CG B:LYS39 4.1 20.0 1.0
N B:ASP105 4.2 40.8 1.0
CE B:LYS39 4.4 20.0 1.0
CB B:ASP105 4.6 44.1 1.0
NZ B:LYS39 4.6 20.0 1.0
N B:VAL106 4.7 40.2 1.0
CB B:ASP104 4.7 46.2 1.0
CA B:ASP105 4.9 42.9 1.0
O B:HOH329 4.9 53.5 1.0
C B:ILE38 5.0 52.0 1.0
CA B:ASP104 5.0 43.9 1.0

Reference:

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
Page generated: Mon Dec 14 07:06:04 2020

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