Zinc in PDB 7yi3: Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex

All present enzymatic activity of Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex:
3.5.1.98;

The binding sites of Zinc atom in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex (pdb code 7yi3). 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 RPD3S in Close-State RPD3S-Ncp Complex, PDB code: 7yi3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex


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 RPD3S in Close-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:44.8 occ:1.00 OD2 B:ASP186 2.0 27.7 1.0 ND1 B:HIS188 2.3 16.6 1.0 OD1 B:ASP186 2.3 31.1 1.0 CG B:ASP186 2.4 23.2 1.0 OD2 B:ASP274 2.4 33.8 1.0 CE1 B:HIS188 3.2 27.3 1.0 CG B:HIS188 3.3 19.7 1.0 CG B:ASP274 3.5 34.7 1.0 CB B:HIS188 3.6 16.2 1.0 CB B:ASP186 3.7 15.5 1.0 N B:HIS188 4.0 20.5 1.0 OH B:TYR313 4.1 37.6 1.0 CA B:GLY311 4.2 13.7 1.0 CE1 B:HIS150 4.3 26.9 1.0 CB B:ASP274 4.3 25.8 1.0 NE2 B:HIS188 4.3 22.9 1.0 CD2 B:HIS188 4.4 22.9 1.0 OD1 B:ASP274 4.4 28.6 1.0 CA B:HIS188 4.4 18.5 1.0 N B:VAL187 4.6 24.9 1.0 CG2 B:VAL187 4.6 23.6 1.0 N B:GLY311 4.7 22.3 1.0 NE2 B:HIS151 4.7 19.8 1.0 CA B:ASP186 4.8 22.9 1.0 NE2 B:HIS150 4.8 18.6 1.0 C B:ASP186 4.9 35.2 1.0 CZ B:TYR313 5.0 34.8 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex


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 RPD3S in Close-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:81.2 occ:1.00 ND1 D:HIS448 2.1 40.2 1.0 SG D:CYS420 2.3 55.9 1.0 SG D:CYS417 2.3 40.1 1.0 SG D:CYS451 2.3 62.2 1.0 CG D:HIS448 2.6 38.8 1.0 CB D:HIS448 2.8 31.0 1.0 CB D:CYS417 2.9 39.7 1.0 CE1 D:HIS448 3.1 33.1 1.0 CB D:CYS420 3.3 39.0 1.0 CB D:CYS451 3.5 39.9 1.0 CD2 D:HIS448 3.7 36.6 1.0 N D:CYS420 3.8 37.3 1.0 N D:HIS448 3.8 26.6 1.0 CA D:HIS448 3.9 24.8 1.0 NE2 D:HIS448 3.9 29.1 1.0 CA D:CYS420 4.1 36.5 1.0 CA D:CYS417 4.4 39.0 1.0 O D:GLN422 4.6 42.0 1.0 CA D:CYS451 4.7 33.9 1.0 CB D:LYS419 4.8 44.7 1.0 C D:CYS417 4.8 40.4 1.0 N D:LYS419 4.9 45.7 1.0 C D:LYS419 4.9 45.8 1.0 N D:CYS451 4.9 36.8 1.0 C D:TRP447 4.9 36.7 1.0 C D:HIS448 4.9 34.8 1.0 C D:CYS420 5.0 39.5 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex


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 RPD3S in Close-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:113.8 occ:1.00 ND1 D:HIS283 2.1 76.2 1.0 SG D:CYS266 2.3 76.4 1.0 SG D:CYS286 2.3 74.2 1.0 SG D:CYS263 2.3 93.6 1.0 CB D:CYS263 3.0 83.9 1.0 CG D:HIS283 3.0 75.6 1.0 CE1 D:HIS283 3.1 76.5 1.0 CB D:CYS286 3.2 69.3 1.0 CB D:CYS266 3.3 69.2 1.0 CB D:HIS283 3.3 73.4 1.0 N D:CYS266 3.7 74.3 1.0 CA D:CYS266 4.1 72.0 1.0 NE C:ARG300 4.1 41.4 1.0 CD2 D:HIS283 4.2 77.2 1.0 NE2 D:HIS283 4.2 75.2 1.0 N D:HIS283 4.3 71.5 1.0 CA D:HIS283 4.4 72.8 1.0 CA D:CYS263 4.5 82.2 1.0 CA D:CYS286 4.7 67.4 1.0 CB D:ALA265 4.7 71.0 1.0 NH2 C:ARG300 4.7 49.9 1.0 CD C:ARG300 4.7 42.2 1.0 CZ C:ARG300 4.8 46.6 1.0 CG C:ARG300 4.8 41.0 1.0 C D:CYS266 4.8 76.6 1.0 N D:ASN267 4.8 80.4 1.0 C D:ALA265 4.8 72.1 1.0 C D:CYS263 5.0 83.2 1.0 N D:CYS286 5.0 65.3 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex


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 RPD3S in Close-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:154.0 occ:1.00 CB D:CYS306 1.8 107.1 1.0 SG D:CYS303 2.3 108.7 1.0 SG D:CYS306 2.3 110.0 1.0 CB D:CYS278 2.7 105.7 1.0 CB D:CYS303 3.0 103.3 1.0 N D:CYS303 3.0 103.0 1.0 CA D:CYS306 3.2 104.2 1.0 SG D:CYS275 3.5 108.0 1.0 CA D:CYS303 3.5 103.7 1.0 SG D:CYS278 3.7 106.1 1.0 N D:CYS306 3.7 103.0 1.0 CB D:CYS275 3.9 110.6 1.0 CA D:CYS278 4.0 106.6 1.0 N D:CYS278 4.0 104.7 1.0 C D:HIS302 4.1 102.0 1.0 OG1 D:THR277 4.2 111.3 1.0 C D:CYS306 4.3 105.9 1.0 CA D:HIS302 4.3 102.4 1.0 C D:CYS303 4.4 102.5 1.0 CB D:HIS302 4.4 105.2 1.0 O D:CYS303 4.4 104.1 1.0 O D:CYS278 4.7 107.4 1.0 C D:CYS278 4.8 107.0 1.0 N D:LYS307 4.8 102.5 1.0 ND1 D:HIS302 4.9 105.1 1.0 C D:THR277 5.0 108.1 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of RPD3S in Close-State RPD3S-Ncp Complex


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 RPD3S in Close-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn704 b:81.8 occ:1.00 NE2 D:HIS469 2.1 55.4 1.0 SG D:CYS466 2.3 62.8 1.0 SG D:CYS443 2.3 52.1 1.0 SG D:CYS440 2.3 45.4 1.0 CB D:CYS466 3.0 46.7 1.0 CD2 D:HIS469 3.0 50.8 1.0 CE1 D:HIS469 3.1 50.6 1.0 CB D:CYS443 3.4 47.3 1.0 CB D:CYS440 3.5 37.8 1.0 N D:CYS443 3.5 46.9 1.0 N D:CYS466 3.8 41.6 1.0 CA D:CYS466 4.0 43.2 1.0 CA D:CYS443 4.0 45.9 1.0 ND1 D:HIS469 4.2 42.5 1.0 CG D:HIS469 4.2 42.6 1.0 CB D:TYR442 4.3 44.4 1.0 C D:TYR442 4.6 46.0 1.0 N D:TYR442 4.6 47.8 1.0 C D:CYS466 4.6 47.4 1.0 C D:CYS443 4.7 49.6 1.0 O D:CYS466 4.7 56.8 1.0 CA D:TYR442 4.7 41.0 1.0 N D:GLN444 4.8 41.7 1.0 CA D:CYS440 4.9 38.9 1.0 C D:LYS465 5.0 47.5 1.0

H.P.Guan, P.Wang, C.Y.Yan, H.T.Li. Dynamic and Multivalent Engagement Determines Context-Dependent Nucleosomal Deacetylation By the RPD3S Complex To Be Published.