Zinc in PDB 8pp7: Human Rybp-PRC1 Bound to Mononucleosome

All present enzymatic activity of Human Rybp-PRC1 Bound to Mononucleosome:
2.3.2.27;

The binding sites of Zinc atom in the Human Rybp-PRC1 Bound to Mononucleosome (pdb code 8pp7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Rybp-PRC1 Bound to Mononucleosome, PDB code: 8pp7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


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 Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:94.0 occ:1.00 SG K:CYS21 2.3 61.2 1.0 SG K:CYS39 2.3 64.3 1.0 SG K:CYS18 2.3 62.9 1.0 SG K:CYS42 2.3 62.3 1.0 CB K:CYS18 2.9 57.6 1.0 CB K:CYS39 3.2 60.1 1.0 CB K:CYS21 3.3 55.5 1.0 CB K:CYS42 3.5 59.5 1.0 N K:CYS21 3.7 54.9 1.0 N K:CYS39 4.0 59.7 1.0 CA K:CYS21 4.1 55.6 1.0 CA K:CYS39 4.2 59.7 1.0 CA K:CYS18 4.3 58.3 1.0 CB K:LEU20 4.5 56.1 1.0 C K:CYS18 4.7 57.2 1.0 O K:CYS18 4.7 55.9 1.0 C K:LEU20 4.7 55.7 1.0 NH1 L:ARG26 4.7 61.1 1.0 CA K:CYS42 4.9 60.4 1.0 N K:LEU20 4.9 55.9 1.0 CA K:LEU20 4.9 56.0 1.0 N K:GLY22 5.0 53.2 1.0 C K:CYS21 5.0 55.8 1.0 NH2 L:ARG26 5.0 61.8 1.0

Zinc binding site 2 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn402 b:83.9 occ:1.00 ND1 K:HIS36 2.1 58.3 1.0 SG K:CYS53 2.3 61.8 1.0 SG K:CYS56 2.3 63.5 1.0 SG K:CYS34 2.3 58.7 1.0 CE1 K:HIS36 2.5 57.3 1.0 CB K:CYS53 3.2 57.9 1.0 CG K:HIS36 3.2 56.3 1.0 CB K:CYS34 3.3 54.7 1.0 CB K:CYS56 3.7 58.1 1.0 NE2 K:HIS36 3.7 57.9 1.0 N K:CYS56 3.9 57.9 1.0 CB K:HIS36 3.9 55.8 1.0 CD2 K:HIS36 4.0 56.1 1.0 CA K:CYS56 4.3 58.2 1.0 CA K:CYS53 4.6 57.8 1.0 CB K:ILE55 4.7 57.7 1.0 CA K:CYS34 4.8 54.9 1.0 CB K:VAL58 4.9 55.9 1.0 C K:CYS56 4.9 58.7 1.0 N K:ILE55 5.0 58.6 1.0 N K:ASP57 5.0 58.7 1.0 C K:ILE55 5.0 57.9 1.0

Zinc binding site 3 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:101.3 occ:1.00 SG L:CYS72 2.3 60.2 1.0 SG L:CYS54 2.3 60.6 1.0 SG L:CYS51 2.3 69.2 1.0 SG L:CYS75 2.3 58.6 1.0 CB L:CYS51 3.1 63.0 1.0 CB L:CYS54 3.2 59.0 1.0 CB L:CYS72 3.2 55.5 1.0 CB L:CYS75 3.6 52.9 1.0 N L:CYS54 3.7 59.2 1.0 N L:CYS72 4.0 55.7 1.0 CA L:CYS54 4.0 60.2 1.0 CA L:CYS72 4.2 55.6 1.0 CA L:CYS51 4.6 62.5 1.0 CB L:ILE53 4.6 57.6 1.0 C L:ILE53 4.8 57.8 1.0 C L:CYS54 4.9 60.4 1.0 CA L:CYS75 4.9 52.5 1.0

Zinc binding site 4 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn402 b:89.9 occ:1.00 ND1 L:HIS69 2.1 59.6 1.0 SG L:CYS90 2.3 62.7 1.0 SG L:CYS67 2.3 60.7 1.0 SG L:CYS87 2.3 65.4 1.0 CE1 L:HIS69 2.6 60.0 1.0 CG L:HIS69 3.1 57.7 1.0 CB L:CYS67 3.2 56.9 1.0 CB L:CYS87 3.3 58.9 1.0 NE2 L:HIS69 3.7 58.7 1.0 CB L:HIS69 3.8 58.2 1.0 CB L:CYS90 3.8 58.6 1.0 N L:CYS90 3.9 59.8 1.0 CD2 L:HIS69 3.9 57.2 1.0 CB L:THR89 4.3 61.2 1.0 CA L:CYS90 4.4 59.2 1.0 CA L:CYS67 4.6 56.5 1.0 CA L:CYS87 4.8 58.3 1.0 C L:THR89 4.8 62.1 1.0 N L:THR89 4.8 60.6 1.0 CA L:THR89 4.9 62.1 1.0 OG1 L:THR64 4.9 53.3 1.0 CB L:LYS92 5.0 56.6 1.0 OG1 L:THR89 5.0 60.8 1.0 CG2 L:THR89 5.0 60.0 1.0 CG L:LYS92 5.0 56.2 1.0

Zinc binding site 5 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn401 b:96.1 occ:1.00 SG M:CYS21 2.3 58.5 1.0 SG M:CYS39 2.3 60.8 1.0 SG M:CYS18 2.3 61.1 1.0 SG M:CYS42 2.3 59.6 1.0 CB M:CYS39 3.2 54.5 1.0 CB M:CYS18 3.2 55.4 1.0 CB M:CYS21 3.3 56.6 1.0 N M:CYS21 3.7 55.3 1.0 CB M:CYS42 3.7 53.4 1.0 N M:CYS39 3.9 54.8 1.0 CA M:CYS21 4.1 56.3 1.0 CA M:CYS39 4.2 54.6 1.0 CB M:LEU20 4.5 53.1 1.0 C M:LEU20 4.6 53.4 1.0 CA M:CYS18 4.7 55.7 1.0 CA M:LEU20 4.9 52.8 1.0 N M:LEU20 4.9 53.5 1.0 C M:CYS21 5.0 56.0 1.0 C M:PHE38 5.0 53.4 1.0 CA M:CYS42 5.0 53.6 1.0

Zinc binding site 6 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn402 b:84.6 occ:1.00 ND1 M:HIS36 2.1 53.2 1.0 SG M:CYS53 2.3 59.1 1.0 SG M:CYS56 2.3 54.8 1.0 SG M:CYS34 2.3 62.4 1.0 CB M:CYS34 2.8 55.7 1.0 CE1 M:HIS36 2.8 52.2 1.0 CB M:CYS53 3.0 56.6 1.0 CG M:HIS36 3.1 52.8 1.0 CB M:HIS36 3.6 51.5 1.0 CB M:CYS56 3.7 53.4 1.0 NE2 M:HIS36 3.9 52.6 1.0 N M:CYS56 4.0 54.3 1.0 CD2 M:HIS36 4.1 52.3 1.0 CA M:CYS34 4.3 55.0 1.0 CA M:CYS56 4.4 54.5 1.0 CA M:CYS53 4.5 56.3 1.0 CB M:ILE55 4.6 53.6 1.0 C M:CYS34 4.7 54.9 1.0 O M:CYS34 4.8 55.9 1.0 CA M:HIS36 4.8 51.3 1.0 N M:HIS36 4.9 53.0 1.0 C M:CYS53 5.0 55.6 1.0 N M:ILE55 5.0 53.4 1.0 C M:ILE55 5.0 54.1 1.0

Zinc binding site 7 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn401 b:90.9 occ:1.00 SG N:CYS54 2.3 59.2 1.0 SG N:CYS51 2.3 61.0 1.0 SG N:CYS72 2.3 55.4 1.0 SG N:CYS75 2.3 58.0 1.0 CB N:CYS51 3.1 55.9 1.0 CB N:CYS72 3.2 48.9 1.0 CB N:CYS54 3.4 55.5 1.0 CB N:CYS75 3.6 47.8 1.0 N N:CYS54 3.8 54.4 1.0 N N:CYS72 4.1 49.3 1.0 CA N:CYS54 4.2 55.8 1.0 CA N:CYS72 4.3 49.2 1.0 CA N:CYS51 4.6 55.2 1.0 CB N:ILE53 4.7 51.3 1.0 C N:ILE53 4.9 52.3 1.0 CA N:CYS75 4.9 47.9 1.0 C N:CYS54 4.9 56.0 1.0

Zinc binding site 8 out of 8 in the Human Rybp-PRC1 Bound to Mononucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Rybp-PRC1 Bound to Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn402 b:74.6 occ:1.00 ND1 N:HIS69 2.1 48.8 1.0 SG N:CYS67 2.3 51.0 1.0 SG N:CYS87 2.3 56.1 1.0 SG N:CYS90 2.3 58.3 1.0 CE1 N:HIS69 2.6 48.5 1.0 CB N:CYS87 3.1 51.1 1.0 CB N:CYS67 3.1 47.1 1.0 CG N:HIS69 3.3 47.4 1.0 OG1 N:THR89 3.4 52.6 1.0 CB N:CYS90 3.5 52.9 1.0 N N:CYS90 3.8 52.5 1.0 NE2 N:HIS69 3.9 47.7 1.0 CB N:HIS69 3.9 47.4 1.0 CD2 N:HIS69 4.2 46.9 1.0 CA N:CYS90 4.2 53.6 1.0 OG1 N:THR64 4.4 42.1 1.0 CA N:CYS87 4.6 50.6 1.0 CA N:CYS67 4.6 47.9 1.0 CB N:THR89 4.8 52.5 1.0 N N:THR89 4.9 51.6 1.0 C N:CYS90 5.0 53.0 1.0 C N:THR89 5.0 53.3 1.0 N N:ARG91 5.0 53.3 1.0 C N:CYS87 5.0 49.6 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