Zinc in PDB 8pp6: Human Rybp-PRC1 Bound to H2AK118UB1 Nucleosome

The binding sites of Zinc atom in the Human Rybp-PRC1 Bound to H2AK118UB1 Nucleosome (pdb code 8pp6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human Rybp-PRC1 Bound to H2AK118UB1 Nucleosome, PDB code: 8pp6:

Zinc binding site 1 out of 1 in the Human Rybp-PRC1 Bound to H2AK118UB1 Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Rybp-PRC1 Bound to H2AK118UB1 Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:178.8 occ:1.00 SG K:CYS27 2.3 133.3 1.0 SG K:CYS44 2.3 137.9 1.0 SG K:CYS30 2.3 141.7 1.0 SG K:CYS41 2.3 135.8 1.0 CB K:CYS27 3.0 131.6 1.0 CB K:CYS41 3.0 128.4 1.0 CB K:CYS30 3.2 140.8 1.0 N K:CYS30 3.5 140.2 1.0 CB K:CYS44 3.8 136.3 1.0 CA K:CYS30 3.9 140.6 1.0 CB K:VAL46 4.4 117.8 1.0 OD1 K:ASN34 4.4 125.6 1.0 CA K:CYS27 4.5 129.1 1.0 CA K:CYS41 4.5 128.4 1.0 CB K:VAL29 4.5 133.2 1.0 N K:CYS44 4.6 135.6 1.0 C K:VAL29 4.7 133.6 1.0 CA K:CYS44 4.7 136.6 1.0 C K:CYS30 4.8 141.6 1.0 N K:VAL29 4.8 133.6 1.0 N K:VAL46 4.8 119.9 1.0 N K:THR31 4.9 142.8 1.0 CG2 K:VAL46 4.9 117.8 1.0 CA K:VAL29 4.9 133.4 1.0 O K:VAL46 4.9 118.1 1.0

M.Ciapponi, E.Karlukova, S.Schkolziger, C.Benda, J.Muller. Structural Basis of the Histone Ubiquitination Read-Write Mechanism of Rybp-PRC1. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 38528151
DOI: 10.1038/S41594-024-01258-X