Zinc in PDB 8bja: Structure of the Human UBR5 Dimer

All present enzymatic activity of Structure of the Human UBR5 Dimer:
2.3.2.26;

The binding sites of Zinc atom in the Structure of the Human UBR5 Dimer (pdb code 8bja). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Human UBR5 Dimer, PDB code: 8bja:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2901 b:102.3 occ:1.00 SG B:CYS1179 2.3 67.0 1.0 SG B:CYS1232 2.3 98.1 1.0 SG B:CYS1208 2.3 69.8 1.0 SG B:CYS1211 2.3 87.2 1.0 CB B:CYS1179 3.0 47.3 1.0 CB B:CYS1232 3.3 80.7 1.0 CB B:CYS1211 3.4 66.5 1.0 CB B:CYS1208 3.4 47.0 1.0 N B:CYS1208 3.8 54.5 1.0 CA B:CYS1179 3.9 51.1 1.0 N B:SER1180 4.1 63.9 1.0 CA B:CYS1208 4.2 52.3 1.0 N B:CYS1211 4.2 63.9 1.0 CA B:CYS1211 4.4 61.2 1.0 ZN B:ZN2902 4.5 123.5 1.0 C B:CYS1179 4.5 61.2 1.0 CB B:CYS1234 4.5 81.1 1.0 CA B:CYS1232 4.7 78.3 1.0 C B:CYS1208 4.8 66.2 1.0 O B:CYS1208 4.9 80.4 1.0 C B:CYS1207 4.9 57.1 1.0

Zinc binding site 2 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2902 b:123.5 occ:1.00 SG B:CYS1240 2.3 86.3 1.0 SG B:CYS1211 2.3 87.2 1.0 SG B:CYS1234 2.3 90.2 1.0 SG B:CYS1215 2.3 85.5 1.0 CB B:CYS1211 3.0 66.5 1.0 CB B:CYS1234 3.2 81.1 1.0 CB B:CYS1215 3.3 63.8 1.0 CB B:CYS1240 3.7 77.9 1.0 CA B:CYS1211 3.8 61.2 1.0 OG1 B:THR1242 4.0 56.1 1.0 CA B:CYS1240 4.0 74.1 1.0 ZN B:ZN2901 4.5 102.3 1.0 CA B:CYS1234 4.5 74.3 1.0 CB B:THR1242 4.6 57.1 1.0 C B:CYS1234 4.6 75.1 1.0 N B:LYS1241 4.7 71.7 1.0 C B:CYS1211 4.7 63.4 1.0 O B:CYS1234 4.8 81.1 1.0 CA B:CYS1215 4.8 58.6 1.0 O B:CYS1211 4.8 76.5 1.0 N B:CYS1211 4.8 63.9 1.0 C B:CYS1240 4.8 78.3 1.0 N B:THR1242 4.9 55.9 1.0 N B:TRP1235 5.0 67.2 1.0

Zinc binding site 3 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2903 b:128.7 occ:1.00 CD2 B:HIS1216 1.3 70.1 1.0 NE2 B:HIS1216 2.0 71.5 1.0 ND1 B:HIS1219 2.0 69.6 1.0 SG B:CYS1196 2.3 77.4 1.0 SG B:CYS1199 2.3 94.1 1.0 CG B:HIS1216 2.5 57.9 1.0 CE1 B:HIS1219 3.0 66.8 1.0 CG B:HIS1219 3.0 64.5 1.0 CE1 B:HIS1216 3.1 63.9 1.0 ND1 B:HIS1216 3.3 53.0 1.0 CB B:HIS1219 3.3 63.9 1.0 CB B:CYS1199 3.4 79.3 1.0 CB B:HIS1216 3.4 58.7 1.0 CB B:CYS1196 3.5 71.6 1.0 N B:CYS1199 3.8 71.5 1.0 NE2 B:HIS1219 4.1 65.8 1.0 CD2 B:HIS1219 4.1 64.5 1.0 CA B:HIS1216 4.2 58.1 1.0 CA B:CYS1199 4.2 74.3 1.0 CB B:THR1198 4.5 64.3 1.0 C B:THR1198 4.7 62.4 1.0 CA B:HIS1219 4.9 59.7 1.0 CA B:CYS1196 4.9 71.1 1.0 CG2 B:THR1198 4.9 68.2 1.0 N B:THR1198 4.9 66.0 1.0 CA B:THR1198 5.0 61.1 1.0

Zinc binding site 4 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2901 b:78.3 occ:1.00 SG A:CYS1232 2.3 84.8 1.0 SG A:CYS1208 2.3 77.9 1.0 SG A:CYS1179 2.3 44.0 1.0 SG A:CYS1211 2.3 86.6 1.0 CB A:CYS1179 2.5 49.3 1.0 CB A:CYS1232 3.3 70.2 1.0 CB A:CYS1211 3.5 66.9 1.0 CA A:CYS1179 3.8 56.0 1.0 N A:SER1180 3.8 63.6 1.0 CB A:CYS1208 3.9 65.1 1.0 N A:CYS1208 4.1 66.4 1.0 C A:CYS1179 4.2 60.3 1.0 ZN A:ZN2902 4.3 108.7 1.0 CB A:CYS1234 4.3 81.0 1.0 N A:CYS1211 4.4 69.0 1.0 CA A:CYS1211 4.5 59.1 1.0 CA A:CYS1208 4.5 62.7 1.0 OG1 A:THR1242 4.6 62.7 1.0 CA A:CYS1232 4.7 66.2 1.0 N A:PHE1181 4.7 51.8 1.0 SG A:CYS1240 4.8 87.0 1.0 CA A:SER1180 4.9 57.5 1.0 N A:CYS1179 4.9 58.5 1.0 O A:CYS1208 5.0 78.4 1.0

Zinc binding site 5 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2902 b:108.7 occ:1.00 SG A:CYS1234 2.3 89.9 1.0 SG A:CYS1240 2.3 87.0 1.0 SG A:CYS1211 2.3 86.6 1.0 SG A:CYS1215 2.3 71.6 1.0 OG1 A:THR1242 3.0 62.7 1.0 CB A:CYS1234 3.1 81.0 1.0 CB A:CYS1211 3.3 66.9 1.0 CB A:CYS1215 3.3 57.9 1.0 CB A:CYS1240 3.4 74.0 1.0 CA A:CYS1240 3.7 70.2 1.0 CA A:CYS1211 4.1 59.1 1.0 ZN A:ZN2901 4.3 78.3 1.0 CB A:THR1242 4.3 55.1 1.0 C A:CYS1240 4.5 72.3 1.0 CA A:CYS1234 4.5 74.5 1.0 N A:LYS1241 4.5 64.9 1.0 CG2 A:THR1242 4.6 59.1 1.0 N A:THR1242 4.7 57.0 1.0 CA A:CYS1215 4.8 46.8 1.0 O A:CYS1211 4.8 68.6 1.0 C A:CYS1234 4.8 82.7 1.0 CB A:CYS1179 4.9 49.3 1.0 N A:CYS1240 4.9 74.8 1.0 C A:CYS1211 5.0 57.1 1.0

Zinc binding site 6 out of 6 in the Structure of the Human UBR5 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Human UBR5 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2903 b:132.1 occ:1.00 ND1 A:HIS1219 2.0 64.6 1.0 ND1 A:HIS1216 2.1 67.5 1.0 SG A:CYS1196 2.3 79.5 1.0 SG A:CYS1199 2.3 102.1 1.0 CE1 A:HIS1216 2.9 66.0 1.0 CE1 A:HIS1219 2.9 63.9 1.0 CG A:HIS1216 3.1 58.6 1.0 CG A:HIS1219 3.2 58.5 1.0 CB A:CYS1199 3.3 88.4 1.0 CB A:HIS1216 3.5 59.3 1.0 CB A:CYS1196 3.6 78.9 1.0 CB A:HIS1219 3.6 61.9 1.0 N A:CYS1199 3.8 81.4 1.0 NE2 A:HIS1216 3.9 60.9 1.0 CD2 A:HIS1216 4.1 58.7 1.0 NE2 A:HIS1219 4.1 62.6 1.0 CA A:HIS1216 4.1 54.6 1.0 CA A:CYS1199 4.2 80.4 1.0 CD2 A:HIS1219 4.2 58.9 1.0 CB A:THR1198 4.3 69.4 1.0 C A:THR1198 4.6 72.1 1.0 CA A:THR1198 4.9 69.2 1.0 O A:CYS1215 4.9 59.6 1.0 CA A:CYS1196 5.0 81.8 1.0 N A:THR1198 5.0 67.8 1.0 CG2 A:THR1198 5.0 72.0 1.0

Z.Hodakova, I.Grishkovskaya, H.L.Brunner, D.L.Bolhuis, K.Belacic, A.Schleiffer, H.Kotisch, N.G.Brown, D.Haselbach. Cryo-Em Structure of the Chain-Elongating E3 Ligase UBR5 To Be Published.