Zinc in PDB 9dgg: NCPRC1RYBP Bound to Unmodified Nucleosome

All present enzymatic activity of NCPRC1RYBP Bound to Unmodified Nucleosome:
2.3.2.27;

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

Zinc binding site 1 out of 4 in the NCPRC1RYBP Bound to Unmodified 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 Unmodified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:187.4 occ:1.00 SG K:CYS21 2.3 124.4 1.0 SG K:CYS39 2.3 130.5 1.0 SG K:CYS18 2.3 135.2 1.0 SG K:CYS42 2.3 120.9 1.0 CB K:CYS39 2.7 115.6 1.0 CB K:CYS18 2.7 128.9 1.0 CB K:CYS21 3.2 118.6 1.0 N K:CYS39 3.5 114.0 1.0 CB K:CYS42 3.5 111.5 1.0 CA K:CYS39 3.7 110.6 1.0 N K:CYS21 3.9 114.2 1.0 CA K:CYS21 4.2 116.7 1.0 CA K:CYS18 4.2 126.3 1.0 C K:CYS18 4.6 126.2 1.0 C K:CYS39 4.7 111.5 1.0 C K:PHE38 4.7 103.1 1.0 O K:CYS18 4.7 128.0 1.0 O K:CYS39 4.7 117.0 1.0 O K:TYR24 4.8 129.2 1.0 O K:GLY23 4.9 138.2 1.0 CA K:CYS42 4.9 105.0 1.0 NH1 L:ARG26 4.9 131.2 1.0 N K:CYS18 5.0 127.7 1.0 C K:CYS21 5.0 117.8 1.0

Zinc binding site 2 out of 4 in the NCPRC1RYBP Bound to Unmodified 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 Unmodified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn402 b:145.3 occ:1.00 ND1 K:HIS36 2.1 100.5 1.0 SG K:CYS56 2.3 126.0 1.0 SG K:CYS53 2.3 122.8 1.0 SG K:CYS34 2.3 114.2 1.0 CE1 K:HIS36 2.6 99.5 1.0 CG K:HIS36 3.0 93.4 1.0 CB K:CYS34 3.2 103.0 1.0 CB K:CYS53 3.2 112.7 1.0 NE2 K:HIS36 3.6 94.7 1.0 CB K:HIS36 3.7 94.1 1.0 CB K:CYS56 3.7 112.0 1.0 N K:CYS56 3.8 101.4 1.0 CD2 K:HIS36 3.8 92.0 1.0 CD1 K:ILE31 4.2 95.8 1.0 CA K:CYS56 4.3 108.3 1.0 CA K:CYS34 4.6 99.6 1.0 CB K:ILE55 4.6 90.9 1.0 CA K:CYS53 4.7 108.6 1.0 CB K:VAL58 4.7 106.7 1.0 C K:CYS56 4.8 109.5 1.0 O K:CYS34 4.8 105.4 1.0 C K:CYS34 4.8 99.6 1.0 CG1 K:ILE31 4.9 94.1 1.0 C K:ILE55 4.9 95.8 1.0 N K:ILE55 4.9 96.7 1.0 N K:VAL58 4.9 101.6 1.0 N K:ASP57 5.0 110.4 1.0

Zinc binding site 3 out of 4 in the NCPRC1RYBP Bound to Unmodified 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 Unmodified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:187.7 occ:1.00 SG L:CYS72 2.3 129.1 1.0 SG L:CYS54 2.3 126.0 1.0 SG L:CYS51 2.3 131.5 1.0 SG L:CYS75 2.3 119.2 1.0 CB L:CYS51 2.8 120.7 1.0 CB L:CYS54 3.2 113.5 1.0 CB L:CYS72 3.3 115.5 1.0 CB L:CYS75 3.4 109.8 1.0 N L:CYS54 3.7 107.3 1.0 N L:CYS72 4.0 117.7 1.0 CA L:CYS54 4.1 110.9 1.0 CA L:CYS72 4.2 113.3 1.0 CA L:CYS51 4.3 112.3 1.0 CB L:ILE53 4.7 109.7 1.0 CA L:CYS75 4.8 106.2 1.0 C L:ILE53 4.8 105.3 1.0 C L:CYS54 4.9 111.1 1.0 C L:CYS51 4.9 109.4 1.0

Zinc binding site 4 out of 4 in the NCPRC1RYBP Bound to Unmodified 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 Unmodified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn402 b:147.7 occ:1.00 ND1 L:HIS69 2.1 108.1 1.0 SG L:CYS67 2.3 118.7 1.0 SG L:CYS87 2.3 136.4 1.0 SG L:CYS90 2.3 125.6 1.0 CE1 L:HIS69 2.6 105.3 1.0 OG1 L:THR89 3.0 115.5 1.0 CB L:CYS67 3.0 104.8 1.0 CB L:CYS87 3.2 121.0 1.0 CG L:HIS69 3.3 107.0 1.0 CB L:CYS90 3.3 116.9 1.0 N L:CYS90 3.6 107.5 1.0 NE2 L:HIS69 3.8 105.3 1.0 CB L:HIS69 3.9 104.1 1.0 CA L:CYS90 4.0 112.1 1.0 CD2 L:HIS69 4.1 106.1 1.0 CB L:THR89 4.3 109.5 1.0 OG1 L:THR64 4.4 101.0 1.0 CA L:CYS67 4.5 98.7 1.0 C L:THR89 4.6 109.1 1.0 CA L:CYS87 4.6 116.4 1.0 C L:CYS90 4.7 110.9 1.0 N L:THR89 4.8 111.3 1.0 CA L:THR89 4.8 110.0 1.0 N L:ARG91 4.9 106.1 1.0 C L:CYS67 5.0 100.2 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.