Zinc in PDB 9c5e: Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin

All present enzymatic activity of Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin:
2.3.2.31;

The binding sites of Zinc atom in the Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin (pdb code 9c5e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin, PDB code: 9c5e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:15.0 occ:1.00 NE2 A:HIS479 1.8 15.0 1.0 SG A:CYS475 2.2 15.0 1.0 SG A:CYS467 2.2 15.0 1.0 SG A:CYS464 2.6 15.0 1.0 CD2 A:HIS479 2.9 15.0 1.0 CE1 A:HIS479 2.9 15.0 1.0 HA A:CYS475 3.0 0.0 1.0 CB A:CYS475 3.2 15.0 1.0 HD2 A:HIS479 3.2 0.0 1.0 HB3 A:CYS475 3.2 0.0 1.0 HE1 A:HIS479 3.2 0.0 1.0 HG A:CYS467 3.4 0.0 1.0 HG A:CYS475 3.5 0.0 1.0 CA A:CYS475 3.6 15.0 1.0 HG A:CYS464 3.6 0.0 1.0 HB2 A:CYS467 3.6 0.0 1.0 CB A:CYS467 3.6 15.0 1.0 CB A:CYS464 3.7 15.0 1.0 HB3 A:CYS464 3.8 0.0 1.0 HB2 A:CYS464 3.9 0.0 1.0 ND1 A:HIS479 4.0 15.0 1.0 H A:CYS467 4.0 15.0 1.0 CG A:HIS479 4.0 15.0 1.0 HB2 A:CYS475 4.2 0.0 1.0 HB A:VAL466 4.2 0.0 1.0 HB3 A:CYS467 4.3 0.0 1.0 N A:CYS475 4.5 15.0 1.0 N A:CYS467 4.5 15.0 1.0 CA A:CYS467 4.7 15.0 1.0 O A:CYS475 4.7 15.0 1.0 HB2 A:ALA478 4.7 0.0 1.0 C A:CYS475 4.7 15.0 1.0 HZ3 A:TRP471 4.8 0.0 1.0 H A:CYS475 4.9 15.0 1.0 HD1 A:HIS479 4.9 15.0 1.0

Zinc binding site 2 out of 2 in the Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:15.0 occ:1.00 SG A:CYS454 2.1 15.0 1.0 SG A:CYS459 2.1 15.0 1.0 SG A:CYS436 2.2 15.0 1.0 SG A:CYS439 2.3 15.0 1.0 CB A:CYS454 2.9 15.0 1.0 HB3 A:CYS459 2.9 0.0 1.0 CB A:CYS459 2.9 15.0 1.0 HB3 A:CYS454 3.0 0.0 1.0 HB2 A:CYS454 3.0 0.0 1.0 HB2 A:CYS459 3.2 0.0 1.0 CB A:CYS436 3.2 15.0 1.0 HB3 A:CYS436 3.2 0.0 1.0 HG A:CYS454 3.4 0.0 1.0 HG A:CYS439 3.4 0.0 1.0 HG A:CYS436 3.4 0.0 1.0 HB2 A:CYS436 3.5 0.0 1.0 HG A:CYS459 3.5 0.0 1.0 HB3 A:PHE461 3.5 0.0 1.0 HB3 A:ARG456 3.6 0.0 1.0 CB A:CYS439 3.7 15.0 1.0 HB3 A:CYS439 3.8 0.0 1.0 HB3 A:LYS438 3.8 0.0 1.0 H A:CYS439 4.3 15.0 1.0 CA A:CYS454 4.3 15.0 1.0 H A:PHE461 4.3 15.0 1.0 N A:CYS439 4.3 15.0 1.0 CA A:CYS459 4.4 15.0 1.0 H A:ARG456 4.4 15.0 1.0 HB2 A:CYS439 4.5 0.0 1.0 CB A:PHE461 4.5 15.0 1.0 HA A:CYS454 4.5 0.0 1.0 HD2 A:PHE461 4.5 0.0 1.0 CB A:ARG456 4.6 15.0 1.0 CA A:CYS439 4.6 15.0 1.0 HB A:THR441 4.6 0.0 1.0 CA A:CYS436 4.6 15.0 1.0 HB2 A:PHE461 4.6 0.0 1.0 O A:CYS454 4.7 15.0 1.0 HB2 A:ARG456 4.7 0.0 1.0 HA A:CYS459 4.7 0.0 1.0 HD3 A:LYS438 4.8 0.0 1.0 CB A:LYS438 4.8 15.0 1.0 H A:THR441 4.8 15.0 1.0 C A:CYS454 4.9 15.0 1.0 C A:CYS459 4.9 15.0 1.0 H A:LYS438 4.9 15.0 1.0 O A:CYS436 4.9 15.0 1.0 N A:PHE461 4.9 15.0 1.0 C A:LYS438 4.9 15.0 1.0 O A:ARG456 5.0 15.0 1.0 C A:CYS436 5.0 15.0 1.0

E.M.Connelly, A.C.Rintala-Dempsey, M.Gundogdu, E.A.Freeman, J.Koszela, J.D.Aguirre, G.Zhu, O.Kamarainen, R.Tadayon, H.Walden, G.S.Shaw. Capturing the Catalytic Intermediates of Parkin Ubiquitination. Proc.Natl.Acad.Sci.Usa V. 121 14121 2024.
ISSN: ESSN 1091-6490
PubMed: 39078678
DOI: 10.1073/PNAS.2403114121