Sodium in PDB 6hem: Structure of the C-Terminal Domain of USP25 (748-1048)

All present enzymatic activity of Structure of the C-Terminal Domain of USP25 (748-1048):
3.4.19.12;

The structure of Structure of the C-Terminal Domain of USP25 (748-1048), PDB code: 6hem was solved by M.Gersch, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.56 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.957, 78.288, 84.909, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20.9

The binding sites of Sodium atom in the Structure of the C-Terminal Domain of USP25 (748-1048) (pdb code 6hem). 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 Structure of the C-Terminal Domain of USP25 (748-1048), PDB code: 6hem:

Sodium binding site 1 out of 1 in the Structure of the C-Terminal Domain of USP25 (748-1048)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the C-Terminal Domain of USP25 (748-1048) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:22.7 occ:1.00 O A:THR800 2.2 18.6 1.0 O A:HOH1357 2.3 42.4 1.0 O A:PRO797 2.4 21.6 1.0 OG1 A:THR796 2.4 20.2 1.0 O A:HOH1449 2.5 34.0 1.0 O A:HOH1377 2.8 35.1 1.0 O A:THR796 3.3 20.8 1.0 CB A:THR796 3.4 20.6 1.0 C A:THR800 3.4 15.7 1.0 C A:PRO797 3.4 29.2 1.0 C A:THR796 3.5 16.2 1.0 CA A:THR796 4.0 16.4 1.0 N A:PRO797 4.1 22.6 1.0 CA A:PRO798 4.1 21.2 1.0 O A:HOH1412 4.1 37.5 1.0 N A:THR800 4.2 16.4 1.0 N A:PRO798 4.2 27.1 1.0 C A:PRO798 4.2 18.5 1.0 O A:PRO798 4.3 22.0 1.0 O A:HOH1361 4.3 18.4 1.0 N A:ASP801 4.3 12.7 1.0 CA A:THR800 4.3 15.9 1.0 CA A:PRO797 4.3 25.9 1.0 CA A:ASP801 4.4 12.1 1.0 N A:THR796 4.6 22.2 1.0 CG2 A:THR796 4.6 21.2 1.0 O A:HOH1402 4.7 33.6 1.0 O A:HOH1247 4.7 24.8 1.0 CB A:THR800 4.7 20.2 1.0 CB A:ASP801 4.8 14.1 1.0 N A:GLU799 4.9 17.6 1.0

M.Gersch, J.L.Wagstaff, A.V.Toms, B.Graves, S.M.V.Freund, D.Komander. Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Mol.Cell V. 74 436 2019.
ISSN: ISSN 1097-2765
PubMed: 30926242
DOI: 10.1016/J.MOLCEL.2019.02.030