Sodium in PDB 9ewp: Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain

All present enzymatic activity of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain:
2.3.2.23;

The structure of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain, PDB code: 9ewp was solved by A.Swarnkar, A.Stein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 1.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.139, 44.169, 97.578, 90, 90, 90
R / Rfree (%)	13.5 / 15.6

The structure of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Cadmium	(Cd)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain (pdb code 9ewp). 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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain, PDB code: 9ewp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:40.0 occ:0.82 OD1 A:ASP32 2.4 39.3 1.0 OD2 A:ASP32 2.5 39.9 1.0 CG A:ASP32 2.8 36.9 1.0 O A:HOH318 3.0 33.2 1.0 O A:HOH451 4.1 42.6 1.0 CB A:ASP32 4.2 29.7 1.0 HB2 A:GLU31 4.2 27.3 1.0 O A:HOH308 4.3 24.8 1.0 O A:HOH392 4.3 46.5 1.0 HB2 A:ASP32 4.6 35.7 1.0 HB3 A:GLU31 4.7 27.3 1.0 HB3 A:ASP32 4.7 35.7 1.0 HA A:ASP32 4.8 28.8 1.0 N A:ASP32 4.8 20.6 1.0 CA A:ASP32 4.9 24.0 1.0 H A:ASP32 4.9 24.7 1.0 CB A:GLU31 4.9 22.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:31.8 occ:0.52 O A:HOH380 2.2 27.5 1.0 OE2 A:GLU31 2.4 30.5 1.0 OE1 A:GLU31 2.5 31.9 1.0 CD A:GLU31 2.8 29.5 1.0 O A:HOH406 2.9 38.4 1.0 O A:HOH308 4.1 24.8 1.0 CG A:GLU31 4.3 25.4 1.0 HB2 A:GLU31 4.6 27.3 1.0 HG3 A:GLU31 4.6 30.5 1.0 HG2 A:GLU31 4.8 30.5 1.0 CB A:GLU31 4.9 22.7 1.0 O A:HOH385 5.0 28.2 1.0 O A:HOH364 5.0 23.9 1.0

A.Swarnkar, F.Leidner, A.K.Rout, S.Ainatzi, C.C.Schmidt, S.Becker, H.Urlaub, C.Griesinger, H.Grubmuller, A.Stein. Determinants of Chemoselectivity in Ubiquitination By the J2 Family of Ubiquitin-Conjugating Enzymes Embo J. 2024.
ISSN: ESSN 1460-2075
DOI: 10.1038/S44318-024-00301-3