Sodium in PDB 3ljq: Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor

All present enzymatic activity of Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor:
3.5.1.26;

The structure of Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor, PDB code: 3ljq was solved by Y.Wang, H.-C.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.74 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.061, 52.533, 61.933, 81.47, 90.21, 104.93
R / Rfree (%)	15.4 / 19.7

The binding sites of Sodium atom in the Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor (pdb code 3ljq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor, PDB code: 3ljq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na597 b:13.9 occ:1.00 O A:VAL51 2.3 10.6 1.0 O A:ASP45 2.3 14.8 1.0 O A:TYR53 2.4 11.6 1.0 O A:GLU48 2.5 16.2 1.0 O A:VAL42 2.9 10.8 1.0 C A:ASP45 3.3 14.7 1.0 C A:VAL51 3.5 11.1 1.0 C A:TYR53 3.5 12.5 1.0 C A:GLU48 3.6 15.1 1.0 O A:GLU43 3.7 9.0 1.0 N A:TYR53 3.7 12.1 1.0 CB A:GLU48 3.8 16.8 1.0 N A:ASP45 3.9 13.0 1.0 C A:GLY52 4.0 11.6 1.0 C A:GLU43 4.1 8.5 1.0 C A:VAL42 4.1 10.1 1.0 CA A:GLU48 4.1 16.4 1.0 N A:GLU48 4.1 16.5 1.0 CA A:ASP45 4.1 14.8 1.0 N A:PRO46 4.2 16.0 1.0 CA A:TYR53 4.2 12.3 1.0 CA A:PRO46 4.2 15.7 1.0 CA A:GLU43 4.4 7.9 1.0 N A:GLY52 4.4 12.4 1.0 CA A:VAL51 4.4 9.7 1.0 CA A:GLY52 4.4 11.9 1.0 O A:GLY52 4.5 10.1 1.0 CB A:VAL51 4.5 9.6 1.0 CB A:ASP45 4.5 14.7 1.0 N A:VAL51 4.5 11.1 1.0 N A:GLY54 4.6 11.5 1.0 C A:PRO46 4.6 16.6 1.0 CB A:TYR53 4.6 15.2 1.0 N A:GLU43 4.7 8.0 1.0 C A:ASP44 4.8 13.8 1.0 N A:ARG49 4.8 14.3 1.0 CA A:GLY54 4.8 11.5 1.0 N A:ASP44 4.8 9.3 1.0 N A:GLY55 4.9 10.1 1.0 CG A:GLU48 4.9 20.4 1.0 O A:PRO46 4.9 17.1 1.0 C A:GLY54 5.0 11.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Glycosylasparaginase T152C Apo-Precursor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na597 b:16.4 occ:1.00 O C:VAL351 2.2 10.2 1.0 O C:ASP345 2.3 12.8 1.0 O C:TYR353 2.4 9.6 1.0 O C:GLU348 2.4 12.0 1.0 O C:VAL342 3.1 9.5 1.0 C C:ASP345 3.4 14.2 1.0 C C:VAL351 3.4 10.9 1.0 C C:GLU348 3.4 12.1 1.0 C C:TYR353 3.5 8.8 1.0 CB C:GLU348 3.7 14.9 1.0 O C:GLU343 3.7 9.6 1.0 N C:TYR353 3.9 8.7 1.0 CA C:GLU348 3.9 13.2 1.0 C C:GLY352 3.9 9.9 1.0 N C:GLU348 4.0 13.8 1.0 N C:ASP345 4.1 13.7 1.0 C C:GLU343 4.2 8.7 1.0 CA C:TYR353 4.2 9.9 1.0 CA C:ASP345 4.2 14.5 1.0 C C:VAL342 4.3 8.2 1.0 N C:PRO346 4.3 13.7 1.0 CA C:GLY352 4.3 8.8 1.0 CA C:VAL351 4.3 8.8 1.0 O C:GLY352 4.3 9.7 1.0 N C:GLY352 4.3 8.4 1.0 CA C:PRO346 4.3 14.1 1.0 CB C:VAL351 4.4 7.1 1.0 N C:VAL351 4.4 11.0 1.0 CA C:GLU343 4.5 7.5 1.0 N C:GLY354 4.5 8.3 1.0 CB C:ASP345 4.5 17.1 1.0 C C:PRO346 4.5 12.8 1.0 N C:ARG349 4.6 11.4 1.0 CA C:GLY354 4.7 9.4 1.0 CB C:TYR353 4.7 11.2 1.0 N C:GLY355 4.7 8.6 1.0 O C:PRO346 4.8 14.4 1.0 C C:GLY354 4.8 9.7 1.0 N C:GLU343 4.9 6.6 1.0 N C:THR347 5.0 12.5 1.0 C C:ASP344 5.0 13.3 1.0

Y.Wang, H.C.Guo. Crystallographic Snapshot of Glycosylasparaginase Precursor Poised For Autoprocessing. J.Mol.Biol. V. 403 120 2010.
ISSN: ISSN 0022-2836
PubMed: 20800597
DOI: 10.1016/J.JMB.2010.08.038