Zinc in PDB 8ieg: BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex

All present enzymatic activity of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex:
2.3.2.23; 2.3.2.27;

The binding sites of Zinc atom in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex (pdb code 8ieg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex, PDB code: 8ieg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:169.9 occ:1.00 CE1 A:HIS665 1.9 124.1 1.0 ND1 A:HIS665 2.0 124.1 1.0 SG A:CYS683 2.3 99.2 1.0 SG A:CYS663 2.3 128.5 1.0 SG A:CYS686 2.3 114.5 1.0 CB A:CYS663 2.8 128.5 1.0 CB A:CYS686 3.0 114.5 1.0 CB A:CYS683 3.1 99.2 1.0 NE2 A:HIS665 3.2 124.1 1.0 N A:CYS686 3.3 114.5 1.0 CG A:HIS665 3.4 124.1 1.0 CA A:CYS686 3.7 114.5 1.0 CD2 A:HIS665 3.9 124.1 1.0 CA A:CYS663 4.2 128.5 1.0 CB A:THR685 4.4 112.9 1.0 C A:CYS686 4.4 114.5 1.0 CB A:HIS665 4.4 124.1 1.0 O A:CYS663 4.5 128.5 1.0 C A:THR685 4.5 112.9 1.0 CA A:CYS683 4.5 99.2 1.0 N A:ASN687 4.6 106.5 1.0 C A:CYS663 4.6 128.5 1.0 N A:THR685 4.8 112.9 1.0 CA A:THR685 4.8 112.9 1.0 CG2 A:THR685 4.9 112.9 1.0

Zinc binding site 2 out of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:174.1 occ:1.00 SG A:CYS668 2.3 132.9 1.0 SG A:CYS671 2.3 117.6 1.0 SG A:CYS648 2.3 158.8 1.0 SG A:CYS651 2.3 163.1 1.0 CB A:CYS648 2.7 158.8 1.0 CB A:CYS651 3.0 163.1 1.0 CB A:CYS671 3.1 117.6 1.0 N A:CYS651 3.4 163.1 1.0 CB A:CYS668 3.7 132.9 1.0 CA A:CYS651 3.8 163.1 1.0 CA A:CYS648 4.2 158.8 1.0 CA A:CYS671 4.3 117.6 1.0 N A:CYS671 4.3 117.6 1.0 N A:CYS668 4.3 132.9 1.0 CB A:LEU650 4.4 163.6 1.0 O A:CYS648 4.5 158.8 1.0 C A:CYS648 4.5 158.8 1.0 C A:LEU650 4.5 163.6 1.0 CA A:CYS668 4.6 132.9 1.0 ND2 A:ASN654 4.7 172.5 1.0 N A:SER652 4.8 165.0 1.0 C A:CYS651 4.8 163.1 1.0 N A:LEU650 4.8 163.6 1.0 CA A:LEU650 4.8 163.6 1.0 O A:CYS668 4.9 132.9 1.0 N A:CYS648 5.0 158.8 1.0

Zinc binding site 3 out of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:271.5 occ:1.00 ND1 B:HIS665 2.1 173.6 1.0 SG B:CYS683 2.3 180.9 1.0 SG B:CYS663 2.3 165.2 1.0 SG B:CYS686 2.3 190.7 1.0 CE1 B:HIS665 2.6 173.6 1.0 CB B:CYS663 2.7 165.2 1.0 CB B:CYS683 3.3 180.9 1.0 CG B:HIS665 3.3 173.6 1.0 CB B:CYS686 3.5 190.7 1.0 N B:CYS686 3.6 190.7 1.0 NE2 B:HIS665 3.9 173.6 1.0 CB B:HIS665 4.0 173.6 1.0 CA B:CYS686 4.1 190.7 1.0 CA B:CYS663 4.1 165.2 1.0 CD2 B:HIS665 4.2 173.6 1.0 C B:CYS663 4.5 165.2 1.0 C B:CYS686 4.6 190.7 1.0 CB B:THR685 4.7 169.9 1.0 O B:CYS663 4.7 165.2 1.0 N B:HIS665 4.7 173.6 1.0 CA B:CYS683 4.7 180.9 1.0 C B:THR685 4.7 169.9 1.0 CB B:LYS688 4.8 30.0 1.0 N B:ASN687 4.8 189.5 1.0 N B:THR685 4.8 169.9 1.0 N B:LYS688 4.9 186.2 1.0 CA B:THR685 5.0 169.9 1.0

Zinc binding site 4 out of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:248.4 occ:1.00 SG B:CYS671 2.3 200.1 1.0 SG B:CYS668 2.3 189.9 1.0 SG B:CYS651 2.3 193.0 1.0 SG B:CYS648 2.3 200.9 1.0 CB B:CYS648 2.5 200.9 1.0 CB B:CYS651 2.9 193.0 1.0 CB B:CYS671 3.0 200.1 1.0 CB B:CYS668 3.4 189.9 1.0 N B:CYS651 3.5 193.0 1.0 CA B:CYS651 3.8 193.0 1.0 CA B:CYS648 4.0 200.9 1.0 N B:CYS671 4.1 200.1 1.0 CA B:CYS671 4.2 200.1 1.0 N B:CYS668 4.2 189.9 1.0 CB B:ASN654 4.3 187.7 1.0 CA B:CYS668 4.3 189.9 1.0 O B:ASN654 4.3 187.7 1.0 C B:CYS648 4.4 200.9 1.0 CB B:LEU650 4.5 196.4 1.0 C B:LEU650 4.5 196.4 1.0 OD1 B:ASN654 4.7 187.7 1.0 O B:CYS648 4.7 200.9 1.0 N B:LEU650 4.7 196.4 1.0 N B:CYS648 4.7 200.9 1.0 O B:CYS668 4.8 189.9 1.0 CA B:LEU650 4.8 196.4 1.0 C B:CYS651 4.8 193.0 1.0 C B:CYS668 4.8 189.9 1.0 N B:SER652 4.9 187.1 1.0 N B:ASN654 5.0 187.7 1.0 CG B:ASN654 5.0 187.7 1.0

Z.Deng, H.Ai, M.Sun, Z.Tong, Y.Du, Q.Qu, L.Zhang, Z.Xu, S.Tao, Q.Shi, J.B.Li, M.Pan, L.Liu. Mechanistic Insights Into Nucleosomal H2B Monoubiquitylation Mediated By Yeast BRE1-RAD6 and Its Human Homolog RNF20/RNF40-HRAD6A. Mol.Cell 2023.
ISSN: ISSN 1097-2765
PubMed: 37633270
DOI: 10.1016/J.MOLCEL.2023.08.001