Zinc in PDB 8iej: RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex

All present enzymatic activity of RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex:
2.3.2.23; 2.3.2.27;

The binding sites of Zinc atom in the RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex (pdb code 8iej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex, PDB code: 8iej:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RNF20-RNF40/HRAD6A-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 RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:230.5 occ:1.00 SG A:CYS948 2.1 216.6 1.0 SG A:CYS971 2.4 208.9 1.0 SG A:CYS968 2.7 213.8 1.0 NH2 A:ARG954 2.9 208.7 1.0 CB A:CYS968 3.3 213.8 1.0 CB A:CYS948 3.4 216.6 1.0 CB A:CYS951 3.4 217.1 1.0 CB A:CYS971 3.6 208.9 1.0 N A:CYS951 3.6 217.1 1.0 SG A:CYS951 3.7 217.1 1.0 CZ A:ARG954 3.7 208.7 1.0 CB A:CYS950 4.0 213.5 1.0 SG A:CYS950 4.0 213.5 1.0 CA A:CYS951 4.1 217.1 1.0 NE A:ARG954 4.2 208.7 1.0 NH1 A:ARG954 4.4 208.7 1.0 C A:CYS950 4.5 213.5 1.0 CA A:CYS968 4.6 213.8 1.0 N A:CYS968 4.6 213.8 1.0 CB A:ARG954 4.6 208.7 1.0 CA A:CYS950 4.6 213.5 1.0 CA A:CYS948 4.7 216.6 1.0 N A:CYS950 4.7 213.5 1.0 N A:ASN952 4.8 214.0 1.0 CA A:CYS971 4.9 208.9 1.0 C A:CYS951 4.9 217.1 1.0 C A:CYS948 5.0 216.6 1.0

Zinc binding site 2 out of 4 in the RNF20-RNF40/HRAD6A-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 RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:228.2 occ:1.00 CD2 A:HIS965 1.4 200.9 1.0 NE2 A:HIS965 2.3 200.9 1.0 CG A:HIS965 2.6 200.9 1.0 SG A:CYS983 2.8 200.4 1.0 SG A:CYS963 2.9 197.4 1.0 CB A:HIS965 3.4 200.9 1.0 CB A:CYS983 3.4 200.4 1.0 CE1 A:HIS965 3.4 200.9 1.0 ND1 A:HIS965 3.6 200.9 1.0 CB A:CYS963 3.6 197.4 1.0 CB A:CYS986 3.6 200.8 1.0 N A:CYS986 3.7 200.8 1.0 CB A:LYS985 4.0 197.7 1.0 CA A:CYS986 4.2 200.8 1.0 SG A:CYS986 4.2 200.8 1.0 N A:HIS965 4.4 200.9 1.0 CA A:HIS965 4.6 200.9 1.0 C A:LYS985 4.6 197.7 1.0 O A:CYS963 4.6 197.4 1.0 CA A:LYS985 4.7 197.7 1.0 C A:CYS963 4.8 197.4 1.0 C A:CYS986 4.8 200.8 1.0 CA A:CYS983 4.8 200.4 1.0 CA A:CYS963 4.8 197.4 1.0 N A:LYS985 4.9 197.7 1.0 CE2 A:PHE967 4.9 207.0 1.0

Zinc binding site 3 out of 4 in the RNF20-RNF40/HRAD6A-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 RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn1001 b:188.8 occ:1.00 SG M:CYS945 2.3 148.4 1.0 SG M:CYS942 2.3 161.3 1.0 SG M:CYS925 2.3 189.1 1.0 SG M:CYS922 2.3 185.3 1.0 CB M:CYS922 2.9 185.3 1.0 CB M:CYS942 3.4 161.3 1.0 CB M:CYS925 3.4 189.1 1.0 CZ M:ARG928 3.5 174.6 1.0 NH2 M:ARG928 3.5 174.6 1.0 CB M:CYS945 3.5 148.4 1.0 NE M:ARG928 3.6 174.6 1.0 SG M:CYS924 3.7 204.7 1.0 N M:CYS942 3.9 161.3 1.0 NH1 M:ARG928 4.0 174.6 1.0 N M:CYS925 4.1 189.1 1.0 CA M:CYS942 4.1 161.3 1.0 CD M:ARG928 4.2 174.6 1.0 CA M:CYS922 4.3 185.3 1.0 CA M:CYS925 4.4 189.1 1.0 O M:CYS942 4.5 161.3 1.0 C M:CYS922 4.6 185.3 1.0 C M:CYS942 4.6 161.3 1.0 O M:CYS922 4.7 185.3 1.0 CA M:CYS945 4.7 148.4 1.0 N M:CYS945 4.7 148.4 1.0 CG M:ARG928 4.9 174.6 1.0 O M:ARG928 4.9 174.6 1.0

Zinc binding site 4 out of 4 in the RNF20-RNF40/HRAD6A-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 RNF20-RNF40/HRAD6A-Ub/Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn1002 b:164.8 occ:1.00 ND1 M:HIS939 2.1 150.5 1.0 SG M:CYS957 2.3 142.0 1.0 SG M:CYS960 2.3 148.1 1.0 SG M:CYS937 2.3 146.4 1.0 CE1 M:HIS939 2.6 150.5 1.0 CB M:CYS937 2.7 146.4 1.0 CB M:CYS960 3.0 148.1 1.0 N M:CYS960 3.2 148.1 1.0 CB M:CYS957 3.3 142.0 1.0 CG M:HIS939 3.3 150.5 1.0 CA M:CYS960 3.6 148.1 1.0 NE2 M:HIS939 3.9 150.5 1.0 CB M:HIS939 4.0 150.5 1.0 CB M:LYS959 4.2 147.8 1.0 CD2 M:HIS939 4.2 150.5 1.0 CA M:CYS937 4.2 146.4 1.0 C M:CYS960 4.3 148.1 1.0 C M:LYS959 4.3 147.8 1.0 OH A:TYR999 4.6 183.6 1.0 CA M:LYS959 4.6 147.8 1.0 N M:ASN961 4.6 142.8 1.0 N M:LYS959 4.6 147.8 1.0 CG M:LYS959 4.7 147.8 1.0 CA M:CYS957 4.7 142.0 1.0 C M:CYS937 4.7 146.4 1.0 O M:CYS937 4.8 146.4 1.0 CB M:ALA962 4.8 134.9 1.0 N M:ALA962 4.9 134.9 1.0 O M:CYS960 5.0 148.1 1.0 N M:HIS939 5.0 150.5 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