Zinc in PDB 7jzv: Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome

All present enzymatic activity of Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The binding sites of Zinc atom in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome (pdb code 7jzv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome, PDB code: 7jzv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.0 occ:1.00 SG A:CYS44 2.3 0.0 1.0 SG A:CYS27 2.4 0.0 1.0 SG A:CYS47 2.4 0.0 1.0 SG A:CYS24 2.4 0.0 1.0 CB A:CYS44 3.3 0.0 1.0 CB A:CYS27 3.4 0.0 1.0 CB A:CYS24 3.4 0.0 1.0 CB A:CYS47 3.4 0.0 1.0 N A:CYS27 3.8 0.0 1.0 CA A:CYS27 4.2 0.0 1.0 CB A:ILE26 4.4 25.0 1.0 CA A:CYS44 4.6 0.0 1.0 N A:CYS44 4.7 0.0 1.0 CA A:CYS24 4.7 0.0 1.0 C A:ILE26 4.8 25.0 1.0 CA A:CYS47 4.8 0.0 1.0 N A:ILE26 4.9 25.0 1.0 CG2 A:ILE26 4.9 25.0 1.0 CA A:ILE26 4.9 25.0 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:25.0 occ:1.00 NE2 A:HIS41 2.1 0.0 1.0 SG A:CYS64 2.4 0.0 1.0 SG A:CYS61 2.4 0.0 1.0 SG A:CYS39 2.4 0.0 1.0 CD2 A:HIS41 3.0 0.0 1.0 CE1 A:HIS41 3.1 0.0 1.0 CB A:CYS39 3.4 0.0 1.0 CB A:CYS61 3.4 0.0 1.0 CB A:CYS64 3.4 0.0 1.0 N A:CYS64 4.0 0.0 1.0 CG A:HIS41 4.2 0.0 1.0 ND1 A:HIS41 4.2 0.0 1.0 CA A:CYS64 4.2 0.0 1.0 C A:LEU63 4.3 25.0 1.0 CB A:LEU63 4.7 25.0 1.0 CA A:CYS39 4.7 0.0 1.0 CZ A:PHE43 4.7 25.0 1.0 O A:LEU63 4.8 25.0 1.0 CA A:CYS61 4.8 0.0 1.0 CA A:LEU63 4.9 25.0 1.0 C A:CYS64 4.9 0.0 1.0 C A:CYS39 4.9 0.0 1.0 N A:LEU63 4.9 25.0 1.0 CE1 A:PHE43 4.9 25.0 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:25.0 occ:1.00 SG B:CYS53 2.3 0.0 1.0 SG B:CYS71 2.4 0.0 1.0 SG B:CYS50 2.4 0.0 1.0 SG B:CYS74 2.4 0.0 1.0 N B:CYS71 3.1 0.0 1.0 N B:CYS53 3.2 0.0 1.0 CB B:CYS74 3.4 0.0 1.0 CB B:CYS53 3.5 0.0 1.0 CB B:CYS71 3.5 0.0 1.0 CB B:CYS50 3.5 0.0 1.0 CA B:CYS53 3.7 0.0 1.0 CA B:CYS71 3.8 0.0 1.0 C B:ARG52 4.0 25.0 1.0 C B:PHE70 4.1 25.0 1.0 CB B:ARG52 4.1 25.0 1.0 CA B:PHE70 4.2 25.0 1.0 CA B:ARG52 4.5 25.0 1.0 O B:ILE69 4.5 25.0 1.0 NE B:ARG52 4.6 25.0 1.0 N B:ARG52 4.6 25.0 1.0 CA B:CYS50 4.7 0.0 1.0 CA B:CYS74 4.8 0.0 1.0 O B:ARG52 4.8 25.0 1.0 N B:CYS50 4.8 0.0 1.0 NH2 B:ARG52 4.8 25.0 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the BRCA1-UBCH5C/BARD1 E3-E2 Module Bound to A Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:25.0 occ:1.00 ND1 B:HIS68 2.1 0.0 1.0 SG B:CYS86 2.3 0.0 1.0 SG B:CYS66 2.4 0.0 1.0 SG B:CYS83 2.4 0.0 1.0 CE1 B:HIS68 3.0 0.0 1.0 CG B:HIS68 3.2 0.0 1.0 CB B:CYS83 3.4 0.0 1.0 CB B:CYS86 3.4 0.0 1.0 CB B:CYS66 3.4 0.0 1.0 OG1 B:THR88 3.6 25.0 1.0 CB B:HIS68 3.6 0.0 1.0 NE2 B:HIS68 4.1 0.0 1.0 CD2 B:HIS68 4.3 0.0 1.0 O B:CYS66 4.4 0.0 1.0 CB B:THR88 4.5 25.0 1.0 CD2 B:LEU63 4.6 25.0 1.0 CA B:CYS66 4.7 0.0 1.0 C B:CYS66 4.7 0.0 1.0 CA B:CYS86 4.8 0.0 1.0 CA B:CYS83 4.9 0.0 1.0 N B:THR88 5.0 25.0 1.0

S.R.Witus, A.L.Burrell, D.P.Farrell, J.Kang, M.Wang, J.M.Hansen, A.Pravat, L.M.Tuttle, M.D.Stewart, P.S.Brzovic, C.Chatterjee, W.Zhao, F.Dimaio, J.M.Kollman, R.E.Klevit. BRCA1/BARD1 Site-Specific Ubiquitylation of Nucleosomal H2A Is Directed By BARD1 Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-020-00556-4