Zinc in PDB 8c60: Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution:
3.5.1.98;

The structure of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution (pdb code 8c60). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution, PDB code: 8c60:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:140.0 occ:1.00 CD2 B:HIS179 1.7 45.1 1.0 CG B:HIS179 1.8 54.0 1.0 OD1 B:ASP177 2.1 59.0 1.0 NE2 B:HIS179 2.2 43.6 1.0 ND1 B:HIS179 2.3 48.8 1.0 N B:HIS179 2.4 46.8 1.0 CE1 B:HIS179 2.6 49.5 1.0 CB B:HIS179 2.6 55.1 1.0 CG2 B:ILE178 2.7 50.3 1.0 OD2 B:ASP265 2.7 65.3 1.0 CA B:HIS179 3.0 46.3 1.0 CG B:ASP177 3.3 46.9 1.0 C B:ILE178 3.3 47.6 1.0 CG B:ASP265 3.3 62.2 1.0 OD1 B:ASP265 3.6 59.6 1.0 N B:ILE178 3.6 43.5 1.0 CA B:ILE178 3.7 43.9 1.0 OD2 B:ASP177 3.7 41.0 1.0 CB B:ILE178 3.8 40.9 1.0 O B:ILE178 4.2 63.4 1.0 C B:HIS179 4.3 39.0 1.0 C B:ASP177 4.4 36.5 1.0 CB B:ASP177 4.5 44.3 1.0 CB B:ASP265 4.6 55.3 1.0 O B:HIS179 4.7 42.4 1.0 OH B:TYR205 4.7 56.5 1.0 CE1 B:TYR205 4.8 50.9 1.0 CG1 B:ILE178 4.8 45.3 1.0 CA B:ASP177 4.9 31.8 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:148.6 occ:1.00 CD2 C:HIS318 1.8 83.0 1.0 NE2 C:HIS318 2.1 81.6 1.0 SG C:CYS315 2.3 99.9 1.0 SG C:CYS292 2.3 76.9 1.0 SG C:CYS289 2.3 98.3 1.0 CB C:CYS315 2.9 80.7 1.0 CG C:HIS318 3.1 77.2 1.0 CB C:CYS289 3.2 89.5 1.0 CE1 C:HIS318 3.4 83.2 1.0 CB C:CYS292 3.7 76.5 1.0 ND1 C:HIS318 3.8 85.2 1.0 N C:CYS292 3.9 76.8 1.0 CA C:CYS315 4.1 79.2 1.0 N C:CYS315 4.1 78.6 1.0 CB C:HIS318 4.2 70.0 1.0 O C:CYS292 4.3 83.8 1.0 CA C:CYS292 4.4 76.6 1.0 CD1 C:TYR291 4.5 73.6 1.0 N C:HIS318 4.6 63.1 1.0 CB C:TYR291 4.7 74.3 1.0 CA C:CYS289 4.7 86.9 1.0 C C:CYS315 4.7 84.0 1.0 C C:CYS292 4.8 76.4 1.0 ND2 A:ASN326 4.8 89.8 1.0 C C:TYR291 4.8 80.4 1.0 O C:CYS315 4.8 92.8 1.0 CA C:HIS318 5.0 68.1 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1102 b:100.7 occ:1.00 ND1 C:HIS297 2.1 54.4 1.0 SG C:CYS300 2.3 52.3 1.0 SG C:CYS277 2.3 76.1 1.0 SG C:CYS274 2.3 76.5 1.0 CE1 C:HIS297 2.9 60.7 1.0 CB C:CYS277 3.2 66.1 1.0 CG C:HIS297 3.3 53.9 1.0 CB C:CYS274 3.3 69.7 1.0 CB C:CYS300 3.6 62.9 1.0 CB C:HIS297 3.7 62.3 1.0 N C:CYS277 3.7 60.6 1.0 NE2 C:HIS297 4.1 55.9 1.0 CA C:CYS277 4.1 65.1 1.0 CB C:THR276 4.2 52.2 1.0 CD2 C:HIS297 4.3 51.8 1.0 C C:THR276 4.5 55.5 1.0 NH1 C:ARG279 4.7 63.4 1.0 CA C:THR276 4.7 51.0 1.0 CA C:CYS274 4.8 64.8 1.0 N C:THR276 4.8 52.2 1.0 CG2 C:THR276 4.9 56.4 1.0 CA C:CYS300 4.9 61.8 1.0 N C:HIS297 4.9 65.8 1.0 CA C:HIS297 5.0 63.3 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1103 b:216.4 occ:1.00 SG C:CYS99 2.3 151.7 1.0 SG C:CYS102 2.3 154.5 1.0 SG C:CYS74 2.3 171.2 1.0 SG C:CYS71 2.3 157.1 1.0 CB C:CYS102 3.0 152.2 1.0 CB C:CYS71 3.1 154.9 1.0 CB C:CYS74 3.4 170.7 1.0 CB C:CYS99 3.5 155.2 1.0 N C:CYS74 3.7 172.0 1.0 CA C:CYS74 4.1 171.3 1.0 N C:CYS102 4.1 150.8 1.0 CA C:CYS102 4.2 150.4 1.0 N C:CYS99 4.2 157.3 1.0 CA C:CYS99 4.4 157.3 1.0 CB C:HIS73 4.4 165.6 1.0 O C:CYS74 4.4 170.6 1.0 C C:HIS73 4.5 166.8 1.0 ND1 C:HIS73 4.5 165.2 1.0 CA C:CYS71 4.6 154.4 1.0 C C:CYS74 4.7 171.3 1.0 N C:HIS73 4.8 166.6 1.0 CA C:HIS73 4.8 166.8 1.0 C C:CYS99 5.0 155.6 1.0 CG C:HIS73 5.0 165.7 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1104 b:187.6 occ:1.00 ND1 C:HIS79 2.1 139.1 1.0 SG C:CYS62 2.3 149.4 1.0 SG C:CYS59 2.3 171.8 1.0 SG C:CYS82 2.3 152.3 1.0 OG C:SER61 2.8 154.5 1.0 CG C:HIS79 3.0 136.7 1.0 CE1 C:HIS79 3.1 139.9 1.0 CB C:CYS59 3.1 166.8 1.0 CB C:HIS79 3.2 138.0 1.0 CB C:CYS82 3.4 150.4 1.0 CB C:CYS62 3.7 147.1 1.0 N C:HIS79 3.8 142.5 1.0 N C:CYS62 3.8 150.5 1.0 NZ D:LYS275 4.0 111.6 1.0 CD2 C:HIS79 4.1 137.4 1.0 CA C:HIS79 4.1 141.2 1.0 NE2 C:HIS79 4.1 138.9 1.0 CB C:SER61 4.2 153.2 1.0 CA C:CYS62 4.3 147.7 1.0 CA C:CYS59 4.6 165.8 1.0 C C:SER61 4.8 154.7 1.0 CA C:CYS82 4.8 149.4 1.0 N C:SER61 4.8 158.4 1.0 CA C:SER61 4.9 154.9 1.0 C C:PHE78 4.9 161.0 1.0

M.S.M.Wan, R.Muhammad, M.G.Koliopoulos, T.I.Roumeliotis, J.S.Choudhary, C.Alfieri. Mechanism of Assembly, Activation and Lysine Selection By the SIN3B Histone Deacetylase Complex Nat Commun V. 14 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38276-0