Chlorine 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:

Sodium	(Na)	2 atoms
Cadmium	(Cd)	4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain, PDB code: 9ewp:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl210 b:18.8 occ:0.94 CD A:CD206 2.5 16.8 1.0 HE1 A:HIS94 3.0 19.2 1.0 O A:HOH513 3.3 33.6 0.9 CE1 A:HIS94 3.6 16.0 1.0 CL A:CL211 3.6 22.4 0.6 ND1 A:HIS94 3.6 16.7 1.0 O A:HOH362 3.7 16.8 1.0 OD2 A:ASP96 3.7 18.9 1.0 CG A:ASP96 4.7 17.9 1.0 OD1 A:ASP96 4.8 17.8 1.0 NE2 A:HIS94 4.9 16.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl211 b:22.4 occ:0.63 HG1 A:THR97 2.4 21.3 1.0 CD A:CD206 2.4 16.8 1.0 OG1 A:THR97 2.8 17.8 1.0 HG21 A:THR97 3.0 21.5 1.0 HG23 A:THR97 3.1 21.5 1.0 OD1 A:ASP96 3.3 17.8 1.0 OD2 A:ASP96 3.3 18.9 1.0 ND1 A:HIS94 3.3 16.7 1.0 HB3 A:HIS94 3.3 18.5 1.0 CG2 A:THR97 3.4 17.9 1.0 CG A:ASP96 3.6 17.9 1.0 CL A:CL210 3.6 18.8 0.9 CB A:THR97 3.7 17.7 1.0 O A:HOH513 3.8 33.6 0.9 CG A:HIS94 3.9 15.6 1.0 CB A:HIS94 4.1 15.4 1.0 H A:THR97 4.2 20.3 1.0 CE1 A:HIS94 4.2 16.0 1.0 O A:HOH333 4.3 20.7 0.9 HB A:THR97 4.3 21.3 1.0 HG22 A:THR97 4.3 21.5 1.0 HE1 A:HIS94 4.4 19.2 1.0 N A:THR97 4.5 16.9 1.0 HA A:HIS94 4.6 18.1 1.0 HB2 A:HIS94 4.7 18.5 1.0 O A:HOH362 4.7 16.8 1.0 CA A:THR97 4.8 17.3 1.0 CB A:ASP96 4.9 17.3 1.0 CA A:HIS94 4.9 15.0 1.0 CD2 A:HIS94 5.0 15.4 1.0 HB2 A:ASP96 5.0 20.8 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range:

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