Zinc in PDB 8pmq: Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin

All present enzymatic activity of Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin:
2.3.2.23; 2.3.2.27;

The binding sites of Zinc atom in the Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin (pdb code 8pmq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin, PDB code: 8pmq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn501 b:65.8 occ:1.00 ND1 2:HIS381 2.0 27.1 1.0 SG 2:CYS379 2.3 30.0 1.0 SG 2:CYS404 2.3 32.0 1.0 SG 2:CYS401 2.3 29.8 1.0 CE1 2:HIS381 2.5 27.1 1.0 CB 2:CYS401 3.2 29.8 1.0 CG 2:HIS381 3.3 27.1 1.0 NE2 2:HIS381 3.8 27.1 1.0 CB 2:CYS379 4.0 30.0 1.0 CB 2:HIS381 4.1 27.1 1.0 CB 2:CYS404 4.1 32.0 1.0 CD2 2:HIS381 4.2 27.1 1.0 CB 2:VAL406 4.6 33.5 1.0 O 2:CYS379 4.6 30.0 1.0 CA 2:CYS401 4.7 29.8 1.0 N 2:HIS381 4.7 27.1 1.0 C 2:CYS379 4.7 30.0 1.0 CA 2:CYS379 4.8 30.0 1.0 O 2:CYS404 4.9 32.0 1.0 N 2:CYS379 4.9 30.0 1.0 N 2:CYS404 4.9 32.0 1.0 CG2 2:VAL406 4.9 33.5 1.0 CA 2:CYS404 5.0 32.0 1.0

Zinc binding site 2 out of 2 in the Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Module of Yeast Gid E3 Ligase Bound to Multiphosphorylated UBC8~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ 9:Zn601 b:42.2 occ:1.00 NE2 2:HIS356 2.0 26.7 1.0 SG 9:CYS437 2.3 20.2 1.0 SG 9:CYS434 2.3 20.1 1.0 SG 9:CYS395 2.3 29.2 1.0 CD2 2:HIS356 2.8 26.7 1.0 CB 9:CYS434 3.0 20.1 1.0 CE1 2:HIS356 3.2 26.7 1.0 O 9:CYS395 3.5 29.2 1.0 CB 9:CYS395 3.6 29.2 1.0 CA 9:CYS395 3.8 29.2 1.0 CB 9:CYS437 3.9 20.2 1.0 CG1 9:VAL436 3.9 15.8 1.0 CG 2:HIS356 4.1 26.7 1.0 C 9:CYS395 4.1 29.2 1.0 ND1 2:HIS356 4.2 26.7 1.0 N 9:CYS437 4.3 20.2 1.0 CA 9:CYS437 4.5 20.2 1.0 CA 9:CYS434 4.5 20.1 1.0 C 9:VAL436 4.9 15.8 1.0 OG1 9:THR392 4.9 20.7 1.0

J.Chrustowicz, D.Sherpa, J.Li, C.R.Langlois, E.C.Papadopoulou, D.T.Vu, L.A.Hehl, O.Karayel, V.Beier, S.Von Gronau, J.Muller, J.R.Prabu, M.Mann, G.Kleiger, A.F.Alpi, B.A.Schulman. Multisite Phosphorylation Dictates Selective E2-E3 Pairing As Revealed By UBC8/UBE2H-Gid/Ctlh Assemblies. Mol.Cell 2023.
ISSN: ISSN 1097-2765
PubMed: 38113892
DOI: 10.1016/J.MOLCEL.2023.11.027