Zinc in PDB 6yub: Crystal Structure of UBA4 From Chaetomium Thermophilum

The structure of Crystal Structure of UBA4 From Chaetomium Thermophilum, PDB code: 6yub was solved by P.Grudnik, M.Pabis, K.Ethiraju Ravichandran, S.Glatt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.750, 74.170, 103.660, 90.00, 106.36, 90.00
R / Rfree (%)	20.8 / 25.3

The binding sites of Zinc atom in the Crystal Structure of UBA4 From Chaetomium Thermophilum (pdb code 6yub). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of UBA4 From Chaetomium Thermophilum, PDB code: 6yub:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of UBA4 From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of UBA4 From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.6 occ:1.00 SG A:CYS188 2.3 45.8 0.8 SG A:CYS283 2.3 45.5 1.0 SG A:CYS280 2.3 49.7 1.0 SG A:CYS185 2.4 37.6 0.9 H A:CYS188 2.7 48.6 1.0 H A:CYS185 2.9 51.7 1.0 HB3 A:CYS185 3.0 50.1 0.9 CB A:CYS185 3.2 41.8 1.0 HB2 A:CYS280 3.2 56.2 1.0 CB A:CYS280 3.3 46.8 1.0 H A:CYS283 3.3 62.2 1.0 N A:CYS188 3.4 40.5 1.0 HB3 A:CYS280 3.4 56.2 1.0 CB A:CYS188 3.4 41.5 1.0 HB2 A:CYS188 3.4 49.8 0.8 HB3 A:CYS283 3.5 61.0 1.0 HB2 A:ARG187 3.5 46.8 1.0 CB A:CYS283 3.6 50.9 1.0 N A:CYS185 3.6 43.1 1.0 CA A:CYS188 3.8 41.5 1.0 CA A:CYS185 3.9 42.6 1.0 HB3 A:ALA282 4.0 57.7 1.0 HA A:CYS188 4.0 49.8 1.0 HB2 A:CYS185 4.0 50.1 0.9 N A:CYS283 4.0 51.8 1.0 H A:ARG187 4.1 39.9 1.0 HB3 A:CYS188 4.2 49.8 0.8 C A:CYS185 4.2 41.8 1.0 HB2 A:CYS283 4.3 61.0 1.0 HG3 A:ARG276 4.3 55.4 1.0 C A:ARG187 4.4 36.9 1.0 CA A:CYS283 4.4 52.9 1.0 H A:ALA282 4.4 60.0 1.0 CB A:ARG187 4.4 39.0 1.0 O A:CYS185 4.4 44.3 1.0 H A:LYS277 4.4 54.4 1.0 N A:ARG187 4.6 33.3 1.0 HA A:PRO184 4.6 50.4 1.0 HB3 A:ARG187 4.7 46.8 1.0 HG21 A:VAL147 4.7 46.1 1.0 O A:HOH648 4.7 78.5 1.0 CA A:ARG187 4.7 35.0 1.0 CA A:CYS280 4.7 51.8 1.0 HE A:ARG276 4.7 53.3 1.0 HA A:CYS185 4.8 51.1 1.0 C A:PRO184 4.8 40.2 1.0 HA A:ARG276 4.8 59.4 1.0 HB2 A:LYS277 4.8 68.3 1.0 H A:GLY284 4.9 62.5 1.0 CB A:ALA282 4.9 48.1 1.0 O A:HOH645 4.9 36.4 1.0 HA A:CYS280 4.9 62.2 1.0 N A:TYR186 5.0 41.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of UBA4 From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of UBA4 From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:38.9 occ:1.00 SG B:CYS283 2.2 34.9 1.0 SG B:CYS185 2.3 36.2 1.0 SG B:CYS188 2.3 47.0 1.0 SG B:CYS280 2.3 43.4 0.9 H B:CYS188 2.7 57.7 1.0 HB3 B:CYS185 2.9 46.1 1.0 H B:CYS185 2.9 41.7 1.0 CB B:CYS185 3.1 38.4 1.0 H B:CYS283 3.2 51.4 1.0 HB2 B:CYS280 3.3 53.6 0.9 CB B:CYS280 3.3 44.6 1.0 N B:CYS188 3.3 48.1 1.0 HB3 B:CYS280 3.4 53.6 0.9 HB2 B:ARG187 3.4 48.9 1.0 CB B:CYS188 3.5 49.7 1.0 HB2 B:CYS188 3.6 59.6 1.0 CB B:CYS283 3.7 43.8 1.0 N B:CYS185 3.7 34.8 1.0 HB3 B:CYS283 3.7 52.5 1.0 HB3 B:ALA282 3.8 44.4 1.0 CA B:CYS188 3.8 52.3 1.0 CA B:CYS185 3.8 42.0 1.0 HA B:CYS188 3.9 62.8 1.0 N B:CYS283 4.0 42.9 1.0 HB2 B:CYS185 4.0 46.1 1.0 H B:ARG187 4.1 43.7 1.0 C B:CYS185 4.2 43.3 1.0 CB B:ARG187 4.3 40.8 1.0 C B:ARG187 4.3 47.5 1.0 HB3 B:CYS188 4.3 59.6 1.0 H B:ALA282 4.3 40.0 1.0 O B:CYS185 4.3 38.8 1.0 CA B:CYS283 4.4 44.2 1.0 HB2 B:CYS283 4.4 52.5 1.0 H B:LYS277 4.5 52.7 1.0 N B:ARG187 4.5 36.4 1.0 O B:HOH543 4.5 29.3 1.0 HB3 B:ARG187 4.5 48.9 1.0 HG3 B:ARG276 4.6 61.4 1.0 CA B:ARG187 4.6 41.8 1.0 HG21 B:VAL147 4.6 45.6 1.0 HA B:PRO184 4.7 40.4 1.0 CA B:CYS280 4.7 44.1 1.0 CB B:ALA282 4.7 37.0 1.0 HA B:CYS185 4.7 50.4 1.0 HB2 B:LYS277 4.9 71.7 1.0 C B:PRO184 4.9 34.2 1.0 HA B:ARG276 4.9 60.4 1.0 H B:GLY284 4.9 56.8 1.0 HD2 B:ARG187 4.9 44.4 1.0 N B:TYR186 5.0 39.3 1.0 HA B:CYS280 5.0 52.9 1.0 C B:CYS283 5.0 44.6 1.0

M.Pabis, M.Termathe, K.E.Ravichandran, S.D.Kienast, R.Krutyholowa, M.Sokolowski, U.Jankowska, P.Grudnik, S.A.Leidel, S.Glatt. Molecular Basis For the Bifunctional UBA4-URM1 Sulfur-Relay System in Trna Thiolation and Ubiquitin-Like Conjugation. Embo J. V. 39 05087 2020.
ISSN: ESSN 1460-2075
PubMed: 32901956
DOI: 10.15252/EMBJ.2020105087