Zinc in PDB 9dde: NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome

All present enzymatic activity of NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome:
2.3.2.27;

The binding sites of Zinc atom in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome (pdb code 9dde). 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 H2AK119UB/H1.4 Chromatosome, PDB code: 9dde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome


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 H2AK119UB/H1.4 Chromatosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:205.1 occ:1.00 SG K:CYS21 2.3 171.3 1.0 SG K:CYS39 2.3 170.1 1.0 SG K:CYS18 2.3 172.8 1.0 SG K:CYS42 2.3 171.0 1.0 CB K:CYS18 2.7 170.3 1.0 CB K:CYS39 2.8 169.0 1.0 CB K:CYS21 3.3 167.4 1.0 CB K:CYS42 3.4 167.3 1.0 N K:CYS39 3.7 170.2 1.0 N K:CYS21 3.8 166.1 1.0 CA K:CYS39 3.9 169.1 1.0 CA K:CYS21 4.1 166.9 1.0 CA K:CYS18 4.1 169.9 1.0 O K:CYS18 4.4 169.9 1.0 C K:CYS18 4.5 169.3 1.0 CB K:LEU20 4.6 163.8 1.0 C K:LEU20 4.6 163.7 1.0 CA K:CYS42 4.8 166.8 1.0 NH1 L:ARG26 4.8 166.8 1.0 N K:LEU20 4.9 162.8 1.0 C K:PHE38 4.9 166.6 1.0 C K:CYS39 4.9 168.8 1.0 N K:CYS18 4.9 169.8 1.0 CA K:LEU20 4.9 164.1 1.0 O K:GLY23 5.0 169.1 1.0

Zinc binding site 2 out of 5 in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome


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 H2AK119UB/H1.4 Chromatosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn402 b:205.5 occ:1.00 ND1 K:HIS36 2.1 167.3 1.0 SG K:CYS53 2.3 178.0 1.0 SG K:CYS56 2.3 184.7 1.0 SG K:CYS34 2.3 173.7 1.0 CE1 K:HIS36 2.4 166.3 1.0 CB K:CYS53 3.1 173.2 1.0 CG K:HIS36 3.1 166.2 1.0 CB K:CYS34 3.2 167.9 1.0 NE2 K:HIS36 3.5 165.3 1.0 CB K:CYS56 3.7 182.3 1.0 N K:CYS56 3.8 181.6 1.0 CD2 K:HIS36 3.8 165.4 1.0 CB K:HIS36 4.0 166.8 1.0 CA K:CYS56 4.3 181.7 1.0 CB K:ILE55 4.6 169.7 1.0 CA K:CYS34 4.6 165.8 1.0 CD1 K:ILE31 4.6 151.1 1.0 CA K:CYS53 4.6 172.5 1.0 C K:CYS56 4.8 182.2 1.0 O K:CYS34 4.9 165.6 1.0 N K:ILE55 4.9 171.3 1.0 C K:ILE55 4.9 171.9 1.0 N K:ASP57 4.9 184.3 1.0 C K:CYS34 4.9 164.7 1.0 CB K:VAL58 4.9 172.8 1.0

Zinc binding site 3 out of 5 in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome


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 H2AK119UB/H1.4 Chromatosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:225.2 occ:1.00 SG L:CYS54 2.3 181.5 1.0 SG L:CYS51 2.3 185.2 1.0 SG L:CYS72 2.3 169.1 1.0 SG L:CYS75 2.3 168.7 1.0 CB L:CYS72 2.9 168.5 1.0 CB L:CYS51 3.0 182.2 1.0 CB L:CYS54 3.2 179.1 1.0 CB L:CYS75 3.5 163.8 1.0 N L:CYS54 3.6 178.0 1.0 CA L:CYS54 4.0 179.6 1.0 N L:CYS72 4.0 168.1 1.0 CA L:CYS72 4.1 168.0 1.0 CA L:CYS51 4.5 179.9 1.0 CB L:ILE53 4.5 171.1 1.0 C L:ILE53 4.7 171.5 1.0 C L:CYS54 4.9 180.6 1.0 CA L:CYS75 4.9 161.4 1.0 N L:ILE53 4.9 169.3 1.0 CA L:ILE53 5.0 170.1 1.0

Zinc binding site 4 out of 5 in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome


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 H2AK119UB/H1.4 Chromatosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn402 b:185.2 occ:1.00 ND1 L:HIS69 2.0 154.9 1.0 SG L:CYS90 2.3 157.3 1.0 SG L:CYS87 2.3 170.1 1.0 SG L:CYS67 2.3 152.0 1.0 CE1 L:HIS69 2.4 154.2 1.0 CB L:CYS67 2.8 147.9 1.0 CB L:CYS87 3.1 163.4 1.0 CG L:HIS69 3.2 152.3 1.0 OG1 L:THR89 3.4 165.8 1.0 CB L:CYS90 3.5 155.0 1.0 NE2 L:HIS69 3.5 154.2 1.0 N L:CYS90 3.9 152.6 1.0 CD2 L:HIS69 4.0 152.6 1.0 CB L:HIS69 4.0 151.5 1.0 CA L:CYS90 4.2 153.9 1.0 CA L:CYS67 4.3 145.7 1.0 CA L:CYS87 4.5 160.8 1.0 CB L:LYS92 4.6 151.3 1.0 OG1 L:THR64 4.7 140.7 1.0 C L:CYS90 4.7 154.9 1.0 CB L:THR89 4.8 164.6 1.0 C L:CYS67 4.8 145.4 1.0 N L:LYS92 4.9 153.6 1.0 O L:CYS67 4.9 145.7 1.0 C L:THR89 5.0 162.4 1.0 N L:CYS67 5.0 146.7 1.0

Zinc binding site 5 out of 5 in the NCPRC1RYBP Bound to H2AK119UB/H1.4 Chromatosome


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 H2AK119UB/H1.4 Chromatosome within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn301 b:150.3 occ:1.00 SG M:CYS41 2.3 100.0 1.0 SG M:CYS44 2.3 94.3 1.0 SG M:CYS30 2.3 112.9 1.0 SG M:CYS27 2.3 123.5 1.0 CB M:CYS27 3.1 110.2 1.0 CB M:CYS41 3.4 98.8 1.0 CB M:CYS30 3.4 109.1 1.0 N M:CYS30 3.7 111.3 1.0 CB M:CYS44 3.9 99.1 1.0 CA M:CYS30 4.1 108.6 1.0 CB M:VAL29 4.2 111.8 1.0 N M:CYS44 4.3 103.0 1.0 C M:VAL29 4.5 113.4 1.0 CA M:CYS27 4.6 107.4 1.0 CA M:CYS44 4.7 101.5 1.0 C M:CYS30 4.7 109.1 1.0 CA M:VAL29 4.7 110.8 1.0 N M:VAL29 4.7 106.3 1.0 CA M:CYS41 4.8 96.3 1.0 CG1 M:VAL29 4.9 112.3 1.0 CB M:PHE32 4.9 112.0 1.0 N M:THR31 4.9 111.4 1.0 C M:CYS27 5.0 109.5 1.0

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