Zinc in PDB 7yi2: Cryo-Em Structure of RPD3S in Loose-State RPD3S-Ncp Complex

The binding sites of Zinc atom in the Cryo-Em Structure of RPD3S in Loose-State RPD3S-Ncp Complex (pdb code 7yi2). 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 Loose-State RPD3S-Ncp Complex, PDB code: 7yi2:
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 Loose-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 Loose-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:52.3 occ:1.00 OD2 B:ASP186 2.1 49.2 1.0 OD1 B:ASP186 2.3 54.5 1.0 ND1 B:HIS188 2.3 20.2 1.0 CG B:ASP186 2.5 46.0 1.0 OD2 B:ASP274 2.5 52.9 1.0 CE1 B:HIS188 3.2 34.0 1.0 CG B:HIS188 3.3 33.6 1.0 CG B:ASP274 3.5 44.1 1.0 CB B:HIS188 3.6 32.3 1.0 CB B:ASP274 3.7 38.6 1.0 N B:HIS188 3.9 22.9 1.0 CB B:ASP186 4.0 36.6 1.0 CG1 B:VAL187 4.2 26.0 1.0 CA B:GLY311 4.3 24.2 1.0 CA B:HIS188 4.3 26.4 1.0 N B:VAL187 4.4 45.5 1.0 NE2 B:HIS188 4.4 34.3 1.0 CE1 B:HIS150 4.4 38.7 1.0 CD2 B:HIS188 4.4 35.5 1.0 OD1 B:ASP274 4.6 36.7 1.0 OH B:TYR313 4.6 41.4 1.0 N B:GLY311 4.6 28.6 1.0 NE2 B:HIS150 4.8 29.5 1.0 C B:ASP186 4.8 51.8 1.0 CA B:ASP186 4.8 33.0 1.0 C B:VAL187 4.9 32.1 1.0 NE2 B:HIS151 5.0 29.1 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of RPD3S in Loose-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 Loose-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:112.2 occ:1.00 ND1 D:HIS283 2.1 67.1 1.0 SG D:CYS266 2.3 75.7 1.0 SG D:CYS263 2.3 82.3 1.0 SG D:CYS286 2.3 88.0 1.0 CG D:HIS283 2.6 67.2 1.0 CB D:CYS263 2.8 81.4 1.0 CE1 D:HIS283 2.8 72.1 1.0 CB D:CYS286 3.0 71.2 1.0 CB D:HIS283 3.1 68.8 1.0 CB D:CYS266 3.5 70.9 1.0 CD2 D:HIS283 3.5 71.7 1.0 NE2 D:HIS283 3.6 74.6 1.0 N D:CYS266 3.9 67.3 1.0 N D:HIS283 4.1 64.7 1.0 CA D:HIS283 4.2 67.3 1.0 CA D:CYS263 4.3 77.4 1.0 CA D:CYS266 4.3 71.1 1.0 CA D:CYS286 4.5 71.5 1.0 NE C:ARG300 4.5 38.0 1.0 CB D:ALA265 4.7 74.7 1.0 N D:CYS286 4.8 72.6 1.0 CZ C:ARG300 4.8 43.6 1.0 C D:CYS263 4.9 77.8 1.0 CD C:ARG300 4.9 37.0 1.0 C D:ALA265 4.9 67.2 1.0 NH2 C:ARG300 5.0 47.4 1.0 N D:ALA265 5.0 69.6 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of RPD3S in Loose-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 Loose-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:136.8 occ:1.00 SG D:CYS278 2.3 102.6 1.0 SG D:CYS306 2.3 95.0 1.0 N D:CYS303 2.5 103.4 1.0 CB D:CYS306 2.8 99.1 1.0 CB D:CYS303 3.1 100.3 1.0 SG D:CYS275 3.2 100.4 1.0 CA D:CYS303 3.2 100.2 1.0 OG1 D:THR277 3.3 104.6 1.0 C D:HIS302 3.4 103.3 1.0 SG D:CYS303 3.5 105.1 1.0 CA D:HIS302 3.6 102.2 1.0 CB D:CYS278 3.6 99.2 1.0 O D:CYS303 3.8 99.2 1.0 CB D:HIS302 3.9 103.5 1.0 C D:CYS303 3.9 97.7 1.0 N D:CYS278 4.0 99.8 1.0 CA D:CYS306 4.0 101.0 1.0 N D:CYS306 4.1 100.2 1.0 CB D:CYS275 4.3 96.8 1.0 CA D:CYS278 4.4 99.4 1.0 CB D:THR277 4.5 101.5 1.0 O D:HIS302 4.6 102.2 1.0 CG D:HIS302 4.7 101.5 1.0 O D:CYS278 4.8 96.4 1.0 C D:THR277 4.8 97.8 1.0 N D:HIS302 4.9 97.6 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of RPD3S in Loose-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 Loose-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:126.2 occ:1.00 NE2 D:HIS469 2.1 62.6 1.0 SG D:CYS466 2.3 69.7 1.0 SG D:CYS443 2.3 57.4 1.0 SG D:CYS440 2.3 44.6 1.0 CD2 D:HIS469 2.8 58.3 1.0 CE1 D:HIS469 3.2 58.4 1.0 CB D:CYS466 3.4 54.1 1.0 CB D:CYS440 3.5 48.2 1.0 N D:CYS466 3.6 58.1 1.0 N D:CYS443 3.8 62.0 1.0 CB D:CYS443 3.8 61.0 1.0 CA D:CYS466 4.0 58.4 1.0 CG D:HIS469 4.1 52.5 1.0 ND1 D:HIS469 4.2 48.6 1.0 CB D:TYR442 4.3 56.9 1.0 CA D:CYS443 4.4 65.6 1.0 O D:CYS466 4.6 60.1 1.0 C D:CYS466 4.6 60.7 1.0 C D:LYS465 4.7 57.5 1.0 N D:TYR442 4.7 60.6 1.0 OG1 D:THR445 4.7 57.6 1.0 C D:TYR442 4.8 56.5 1.0 CA D:TYR442 4.8 56.4 1.0 CA D:CYS440 4.8 52.6 1.0 CA D:LYS465 4.9 52.3 1.0 CG D:LYS465 4.9 54.7 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of RPD3S in Loose-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 Loose-State RPD3S-Ncp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn704 b:88.6 occ:1.00 ND1 D:HIS448 2.1 44.8 1.0 SG D:CYS420 2.3 70.5 1.0 SG D:CYS451 2.3 48.0 1.0 SG D:CYS417 2.3 48.0 1.0 CB D:CYS417 3.0 45.1 1.0 CG D:HIS448 3.0 42.0 1.0 CE1 D:HIS448 3.0 42.6 1.0 CB D:CYS420 3.1 50.5 1.0 CB D:HIS448 3.3 39.3 1.0 CB D:CYS451 3.5 42.2 1.0 N D:CYS420 3.5 52.4 1.0 CA D:CYS420 3.9 50.2 1.0 N D:HIS448 4.0 25.8 1.0 NE2 D:HIS448 4.1 41.4 1.0 CD2 D:HIS448 4.1 40.3 1.0 CA D:HIS448 4.3 32.3 1.0 CA D:CYS417 4.4 45.1 1.0 CB D:LYS419 4.4 53.2 1.0 O D:GLN422 4.5 50.0 1.0 C D:LYS419 4.5 56.8 1.0 N D:LYS419 4.7 52.7 1.0 C D:CYS420 4.8 50.8 1.0 C D:CYS417 4.8 50.3 1.0 CA D:LYS419 4.8 58.5 1.0 CA D:CYS451 4.8 37.4 1.0 N D:ASN421 4.9 45.0 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.