Zinc in PDB 7mex: Structure of Yeast UBR1 in Complex with UBC2 and N-Degron

All present enzymatic activity of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron:
2.3.2.23; 2.3.2.27;

The binding sites of Zinc atom in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron (pdb code 7mex). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron, PDB code: 7mex:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:66.2 occ:1.00 ND1 A:HIS157 2.0 47.9 1.0 ND1 A:HIS160 2.0 42.8 1.0 SG A:CYS136 2.3 36.0 1.0 SG A:CYS139 2.3 43.6 1.0 CE1 A:HIS160 2.8 42.8 1.0 CE1 A:HIS157 2.8 47.9 1.0 CB A:CYS139 3.0 43.6 1.0 CG A:HIS160 3.2 42.8 1.0 CG A:HIS157 3.2 47.9 1.0 CB A:CYS136 3.6 36.0 1.0 CB A:HIS157 3.7 47.9 1.0 CB A:HIS160 3.7 42.8 1.0 NE2 A:HIS160 3.9 42.8 1.0 N A:CYS139 4.0 43.6 1.0 NE2 A:HIS157 4.0 47.9 1.0 CA A:CYS139 4.1 43.6 1.0 CD2 A:HIS160 4.1 42.8 1.0 CA A:HIS157 4.2 47.9 1.0 CD2 A:HIS157 4.2 47.9 1.0 O A:ASP156 4.5 50.1 1.0 C A:GLU138 4.5 37.8 1.0 CB A:GLU138 4.8 37.8 1.0 CA A:CYS136 4.9 36.0 1.0 CG2 A:VAL162 4.9 32.3 1.0 CD2 A:LEU187 4.9 49.6 1.0 N A:HIS157 5.0 47.9 1.0

Zinc binding site 2 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:73.7 occ:1.00 SG A:CYS151 2.3 53.2 1.0 SG A:CYS175 2.3 41.4 1.0 SG A:CYS148 2.3 45.3 1.0 SG A:CYS123 2.3 53.1 1.0 CB A:CYS175 3.1 41.4 1.0 CB A:CYS123 3.1 53.1 1.0 CB A:CYS151 3.3 53.2 1.0 CB A:CYS148 3.9 45.3 1.0 CB A:CYS177 4.0 50.1 1.0 ZN A:ZN2003 4.2 112.5 1.0 N A:CYS148 4.2 45.3 1.0 N A:CYS151 4.5 53.2 1.0 CA A:CYS151 4.5 53.2 1.0 CA A:CYS175 4.5 41.4 1.0 CA A:CYS123 4.6 53.1 1.0 CA A:CYS148 4.6 45.3 1.0 CB A:ARG125 4.6 52.2 1.0 NE2 A:HIS118 4.7 77.9 1.0 N A:CYS177 4.8 50.1 1.0 O A:CYS148 5.0 45.3 1.0

Zinc binding site 3 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:112.5 occ:1.00 NE2 A:HIS118 2.0 77.9 1.0 SG A:CYS151 2.2 53.2 1.0 SG A:CYS177 2.3 50.1 1.0 SG A:CYS189 2.3 63.2 1.0 CE1 A:HIS118 2.5 77.9 1.0 CB A:CYS177 3.0 50.1 1.0 CB A:CYS151 3.2 53.2 1.0 CD2 A:HIS118 3.3 77.9 1.0 CB A:CYS189 3.5 63.2 1.0 ND1 A:HIS118 3.7 77.9 1.0 CA A:CYS151 3.8 53.2 1.0 CG A:HIS118 4.2 77.9 1.0 ZN A:ZN2002 4.2 73.7 1.0 CA A:CYS177 4.4 50.1 1.0 CA A:CYS189 4.6 63.2 1.0 CB A:CYS123 4.6 53.1 1.0 N A:CYS151 4.8 53.2 1.0 O A:CYS151 4.8 53.2 1.0 C A:CYS151 4.9 53.2 1.0 SG A:CYS123 4.9 53.1 1.0 C A:CYS177 4.9 50.1 1.0 O A:HIS150 5.0 58.3 1.0

Zinc binding site 4 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:56.3 occ:1.00 NE2 A:HIS1722 2.0 37.9 1.0 SG A:CYS1706 2.3 26.0 1.0 SG A:CYS1727 2.3 33.5 1.0 SG A:CYS1703 2.3 27.3 1.0 CD2 A:HIS1722 2.9 37.9 1.0 CB A:CYS1703 3.0 27.3 1.0 CE1 A:HIS1722 3.1 37.9 1.0 CB A:CYS1727 3.2 33.5 1.0 CB A:CYS1706 3.6 26.0 1.0 CG A:HIS1722 4.1 37.9 1.0 N A:CYS1706 4.2 26.0 1.0 ND1 A:HIS1722 4.2 37.9 1.0 CA A:CYS1706 4.5 26.0 1.0 CA A:CYS1727 4.5 33.5 1.0 CA A:CYS1703 4.5 27.3 1.0 CE1 A:PHE1734 4.8 16.7 1.0 CB A:VAL1708 4.8 36.5 1.0 O A:ASN1726 4.8 44.1 1.0 CB A:THR1705 4.8 22.0 1.0 N A:VAL1708 5.0 36.5 1.0 N A:GLY1707 5.0 29.3 1.0

Zinc binding site 5 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:46.0 occ:1.00 ND1 A:HIS1297 2.0 28.1 1.0 CB A:CYS1323 2.1 28.1 1.0 SG A:CYS1295 2.3 27.1 1.0 SG A:CYS1320 2.4 32.6 1.0 SG A:CYS1323 2.6 28.1 1.0 CE1 A:HIS1297 2.8 28.1 1.0 CB A:CYS1295 2.9 27.1 1.0 CG A:HIS1297 3.2 28.1 1.0 CB A:CYS1320 3.4 32.6 1.0 CA A:CYS1323 3.6 28.1 1.0 CB A:HIS1297 3.7 28.1 1.0 NE2 A:HIS1297 4.0 28.1 1.0 N A:CYS1323 4.0 28.1 1.0 CD2 A:HIS1297 4.2 28.1 1.0 CA A:CYS1295 4.3 27.1 1.0 OG1 A:THR1325 4.5 29.0 1.0 C A:CYS1323 4.5 28.1 1.0 C A:CYS1295 4.6 27.1 1.0 C A:LEU1322 4.8 31.1 1.0 O A:CYS1295 4.8 27.1 1.0 CA A:CYS1320 4.8 32.6 1.0 CG A:PRO1235 4.9 29.4 1.0 N A:HIS1297 4.9 28.1 1.0 CA A:HIS1297 5.0 28.1 1.0 CB A:THR1325 5.0 29.0 1.0

Zinc binding site 6 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2006 b:75.5 occ:1.00 ND1 A:HIS1300 2.0 53.2 1.0 SG A:CYS1223 2.2 67.4 1.0 SG A:CYS1303 2.3 58.3 1.0 SG A:CYS1220 2.3 53.6 1.0 CE1 A:HIS1300 2.9 53.2 1.0 CG A:HIS1300 3.0 53.2 1.0 CB A:CYS1220 3.2 53.6 1.0 CB A:HIS1300 3.4 53.2 1.0 CB A:CYS1303 3.5 58.3 1.0 CB A:CYS1223 3.8 67.4 1.0 NE2 A:HIS1300 4.0 53.2 1.0 N A:CYS1223 4.0 67.4 1.0 CD2 A:HIS1300 4.0 53.2 1.0 O A:CYS1223 4.0 67.4 1.0 N A:HIS1300 4.2 53.2 1.0 CA A:CYS1223 4.3 67.4 1.0 CA A:HIS1300 4.4 53.2 1.0 C A:CYS1223 4.6 67.4 1.0 CB A:SER1226 4.6 80.8 1.0 CA A:CYS1220 4.7 53.6 1.0 CB A:LEU1222 4.8 57.0 1.0 CA A:CYS1303 4.9 58.3 1.0 OG A:SER1226 5.0 80.8 1.0

Zinc binding site 7 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and N-Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Yeast UBR1 in Complex with UBC2 and N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2007 b:65.6 occ:1.00 NE2 A:HIS1763 1.6 25.3 1.0 OD1 A:ASP1775 2.0 28.1 1.0 CD2 A:HIS1763 2.2 25.3 1.0 CG A:ASP1775 2.6 28.1 1.0 OD2 A:ASP1775 2.6 28.1 1.0 NE2 A:HIS161 2.7 32.7 1.0 CE1 A:HIS1763 2.9 25.3 1.0 OD2 A:ASP952 3.0 24.6 1.0 CG A:HIS1763 3.4 25.3 1.0 CD2 A:HIS161 3.5 32.7 1.0 ND1 A:HIS1763 3.7 25.3 1.0 CG A:ASP952 3.8 24.6 1.0 CE1 A:HIS161 3.8 32.7 1.0 OD1 A:ASP952 3.9 24.6 1.0 OH A:TYR933 4.0 18.6 1.0 CB A:ASP1775 4.1 28.1 1.0 CZ A:TYR933 4.3 18.6 1.0 CG2 A:THR948 4.5 26.2 1.0 OG A:SER1762 4.6 24.1 1.0 CE2 A:TYR933 4.7 18.6 1.0 CG A:HIS161 4.7 32.7 1.0 CB A:HIS1763 4.8 25.3 1.0 CE1 A:TYR933 4.8 18.6 1.0 ND1 A:HIS161 4.9 32.7 1.0 CA A:ASP1775 4.9 28.1 1.0

M.Pan, Q.Zheng, T.Wang, L.Liang, Y.Yu, L.Liu, M.Zhao. Structural Insights Into the Initiation and Elongation of Ubiquitination By UBR1 Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-04097-8