Sodium in PDB 8jgu: Crystal Structure of N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans

The structure of Crystal Structure of N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans, PDB code: 8jgu was solved by Y.Zhao, S.Dai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.27 / 1.99
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	101.41, 101.41, 49.26, 90, 90, 120
R / Rfree (%)	18.4 / 21.4

The binding sites of Sodium atom in the Crystal Structure of N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans (pdb code 8jgu). 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 Crystal Structure of N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans, PDB code: 8jgu:

Sodium binding site 1 out of 1 in the Crystal Structure of N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans


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 N-Terminal Domain of Exopolyphosphatase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.6 occ:1.00 OE1 A:GLU143 2.3 28.8 1.0 O A:ASP136 2.9 15.8 1.0 OD2 A:ASP136 3.1 26.3 1.0 N A:GLY138 3.1 18.8 1.0 O A:SER141 3.1 14.9 1.0 O A:HOH509 3.1 26.5 1.0 CD A:GLU143 3.5 23.3 1.0 CA A:GLY138 3.6 19.8 1.0 C A:ASP136 3.7 19.7 1.0 OG A:SER141 3.8 26.7 1.0 O A:HOH587 3.8 29.1 1.0 OE2 A:GLU114 3.8 29.7 1.0 C A:LEU137 3.9 20.4 1.0 C A:SER141 3.9 16.5 1.0 CG A:ASP136 3.9 20.8 1.0 O A:HOH576 4.0 23.4 1.0 OE2 A:GLU143 4.1 25.4 1.0 CD A:GLU114 4.2 24.3 1.0 CA A:LEU137 4.3 15.5 1.0 N A:GLU143 4.3 17.5 1.0 O A:HOH597 4.3 30.5 1.0 N A:LEU137 4.3 18.4 1.0 CB A:ASP136 4.4 17.1 1.0 OE1 A:GLU114 4.4 25.7 1.0 CA A:LEU142 4.5 17.7 1.0 N A:LEU142 4.5 18.4 1.0 CG A:GLU143 4.6 22.5 1.0 O A:LEU137 4.7 20.9 1.0 CA A:ASP136 4.7 18.2 1.0 CB A:GLU143 4.7 19.9 1.0 C A:GLY138 4.7 24.0 1.0 CA A:SER141 4.8 18.8 1.0 C A:LEU142 4.8 18.0 1.0 CB A:SER141 4.8 20.6 1.0 OD1 A:ASP136 4.8 23.7 1.0 N A:SER141 4.9 16.1 1.0

S.Dai, B.Wang, R.Ye, D.Zhang, Z.Xie, N.Yu, C.Cai, C.Huang, J.Zhao, F.Zhang, Y.Hua, Y.Zhao, R.Zhou, B.Tian. Structural Evolution of Bacterial Polyphosphate Degradation Enzyme For Phosphorus Cycling. Adv Sci 09602 2024.
ISSN: ESSN 2198-3844
PubMed: 38682481
DOI: 10.1002/ADVS.202309602