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Sodium in PDB 5ep8: X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion

Enzymatic activity of X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion

All present enzymatic activity of X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion:
2.4.2.2;

Protein crystallography data

The structure of X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion, PDB code: 5ep8 was solved by A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.22 / 2.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.463, 91.350, 109.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 29.3

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion (pdb code 5ep8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion, PDB code: 5ep8:

Sodium binding site 1 out of 1 in 5ep8

Go back to Sodium Binding Sites List in 5ep8
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:54.0
occ:1.00
 O B:GLY88 2.2 53.4 1.0
O B:LEU243 2.5 56.7 1.0
OE1 B:GLU255 2.5 63.2 1.0
O B:ALA246 2.7 44.9 1.0
OG1 B:THR90 2.8 70.2 1.0
C B:GLY88 3.3 54.6 1.0
C B:LEU243 3.5 51.4 1.0
CD B:GLU255 3.7 65.6 1.0
CA B:GLY88 3.8 52.2 1.0
C B:ALA246 3.8 46.2 1.0
CA B:GLY244 3.9 43.7 1.0
N B:ALA246 3.9 47.0 1.0
N B:GLY244 4.1 46.1 1.0
CB B:THR90 4.2 64.8 1.0
CA B:ALA246 4.2 46.4 1.0
C B:GLY244 4.3 45.0 1.0
CB B:ALA246 4.3 43.6 1.0
N B:PHE245 4.3 45.9 1.0
OE1 B:GLU252 4.5 61.4 1.0
N B:THR90 4.5 63.1 1.0
N B:ASP89 4.5 57.2 1.0
OE2 B:GLU255 4.5 71.4 1.0
CD B:GLU252 4.6 55.1 1.0
CG B:GLU255 4.6 64.6 1.0
CG B:GLU252 4.7 54.8 1.0
CA B:LEU243 4.7 54.7 1.0
C B:PHE245 4.8 47.6 1.0
CD2 B:LEU268 4.8 68.4 1.0
CB B:LEU243 4.8 58.3 1.0
CA B:ASP89 4.9 57.7 1.0
CD1 B:LEU268 5.0 67.9 1.0
CA B:THR90 5.0 62.9 1.0
N B:ILE247 5.0 46.5 1.0
C B:ASP89 5.0 62.2 1.0

Reference:

A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure of the Complex Pyrimidine-Nucleoside Phosphorylase From Bacillus Subtilis with Sulfate Ion To Be Published.
Page generated: Sun Aug 17 23:39:55 2025

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