Zinc in PDB 9dby: NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome

All present enzymatic activity of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome:
2.3.2.27;

The binding sites of Zinc atom in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome (pdb code 9dby). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome, PDB code: 9dby:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:201.8 occ:1.00 SG K:CYS21 2.3 156.2 1.0 SG K:CYS39 2.3 151.9 1.0 SG K:CYS18 2.3 145.6 1.0 SG K:CYS42 2.3 142.4 1.0 CB K:CYS39 2.8 148.6 1.0 CB K:CYS21 3.2 151.2 1.0 CB K:CYS18 3.2 145.0 1.0 CB K:CYS42 3.7 142.1 1.0 N K:CYS21 3.8 149.9 1.0 N K:CYS39 3.8 148.6 1.0 CA K:CYS39 3.9 146.9 1.0 CA K:CYS21 4.1 150.2 1.0 CA K:CYS18 4.6 145.3 1.0 C K:LEU20 4.9 134.5 1.0 CB K:LEU20 4.9 133.2 1.0 O K:GLY23 4.9 154.6 1.0 C K:CYS21 4.9 150.8 1.0 C K:CYS18 4.9 145.4 1.0 C K:CYS39 5.0 145.7 1.0 CA K:CYS42 5.0 141.1 1.0

Zinc binding site 2 out of 5 in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn402 b:161.8 occ:1.00 ND1 K:HIS36 2.1 125.6 1.0 SG K:CYS34 2.3 132.2 1.0 SG K:CYS56 2.3 131.9 1.0 SG K:CYS53 2.3 135.0 1.0 CE1 K:HIS36 2.7 125.5 1.0 CG K:HIS36 3.0 123.8 1.0 CB K:CYS34 3.1 124.9 1.0 CB K:CYS53 3.2 129.8 1.0 CB K:HIS36 3.6 121.6 1.0 NE2 K:HIS36 3.7 124.0 1.0 CD2 K:HIS36 3.9 125.2 1.0 CB K:CYS56 3.9 128.6 1.0 N K:CYS56 3.9 125.8 1.0 CG1 K:VAL58 4.1 123.8 1.0 CA K:CYS34 4.5 123.9 1.0 CA K:CYS56 4.5 128.2 1.0 CB K:ILE55 4.5 117.0 1.0 CA K:CYS53 4.7 129.0 1.0 C K:CYS34 4.8 123.2 1.0 O K:CYS34 4.9 125.5 1.0 CA K:HIS36 4.9 122.1 1.0 N K:ILE55 4.9 120.2 1.0 C K:ILE55 5.0 118.3 1.0

Zinc binding site 3 out of 5 in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:188.8 occ:1.00 SG L:CYS54 2.3 157.8 1.0 SG L:CYS51 2.3 155.3 1.0 SG L:CYS72 2.3 134.4 1.0 SG L:CYS75 2.3 132.6 1.0 CB L:CYS72 2.4 134.1 1.0 CB L:CYS51 3.2 151.4 1.0 CB L:CYS54 3.3 154.7 1.0 CB L:CYS75 3.6 128.7 1.0 CA L:CYS72 3.7 130.7 1.0 N L:CYS72 3.8 130.0 1.0 N L:CYS54 3.8 154.0 1.0 CA L:CYS54 4.1 154.1 1.0 CA L:CYS51 4.6 149.8 1.0 C L:CYS72 4.7 132.0 1.0 CB L:ILE53 4.8 144.5 1.0 CD2 L:LEU58 4.8 139.6 1.0 CA L:CYS75 4.9 126.6 1.0 C L:ILE53 4.9 146.1 1.0 C L:CYS54 5.0 154.9 1.0

Zinc binding site 4 out of 5 in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn402 b:155.6 occ:1.00 ND1 L:HIS69 2.1 117.5 1.0 SG L:CYS87 2.3 132.4 1.0 SG L:CYS67 2.3 120.4 1.0 SG L:CYS90 2.3 128.2 1.0 CE1 L:HIS69 2.7 115.6 1.0 CB L:CYS67 2.9 113.7 1.0 CB L:CYS87 3.0 124.9 1.0 CG L:HIS69 3.1 114.9 1.0 OG1 L:THR89 3.3 119.4 1.0 CB L:CYS90 3.6 127.0 1.0 CB L:HIS69 3.7 113.5 1.0 NE2 L:HIS69 3.8 114.2 1.0 N L:CYS90 4.0 121.2 1.0 CD2 L:HIS69 4.0 113.8 1.0 CA L:CYS67 4.3 112.3 1.0 CA L:CYS90 4.4 125.0 1.0 CA L:CYS87 4.5 123.6 1.0 OG1 L:THR64 4.6 106.8 1.0 C L:CYS67 4.6 112.7 1.0 CB L:THR89 4.7 116.8 1.0 O L:CYS67 4.7 112.1 1.0 CB L:LYS92 4.9 123.6 1.0 C L:THR89 4.9 117.0 1.0 N L:HIS69 4.9 113.1 1.0 CA L:HIS69 5.0 112.4 1.0

Zinc binding site 5 out of 5 in the NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of NCPRC1RYBP Bound to Singly Modified H2AK119UB Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn301 b:160.5 occ:1.00 SG M:CYS41 2.3 145.3 1.0 SG M:CYS30 2.3 146.7 1.0 SG M:CYS44 2.3 149.6 1.0 SG M:CYS27 2.3 146.1 1.0 CB M:CYS41 3.2 143.9 1.0 CB M:CYS27 3.3 141.9 1.0 CB M:CYS30 3.6 142.4 1.0 CB M:CYS44 3.7 152.3 1.0 N M:CYS30 3.8 138.3 1.0 N M:CYS44 4.2 151.0 1.0 CA M:CYS30 4.2 139.0 1.0 CA M:CYS44 4.5 152.8 1.0 CB M:VAL29 4.5 138.9 1.0 CA M:CYS41 4.6 145.1 1.0 CG1 M:VAL29 4.6 138.6 1.0 C M:CYS30 4.7 139.1 1.0 CA M:CYS27 4.8 139.3 1.0 C M:VAL29 4.8 136.9 1.0 N M:THR31 4.8 150.0 1.0 N M:VAL29 4.9 136.5 1.0 CA M:VAL29 5.0 137.8 1.0

V.Godinez-Lopez, M.I.Valencia-Sanchez, J.P.Armache, K.-J.Armache. Structural Visualization of Read-Write Mechanisms of Histone H2A Lysine 119 Mono-Ubiquitination By Polycomb Repressive Complex 1 To Be Published.