Zinc in PDB 7z1n: Structure of Yeast Rna Polymerase III Delta C53-C37-C11

All present enzymatic activity of Structure of Yeast Rna Polymerase III Delta C53-C37-C11:
2.7.7.6;

The structure of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11 (pdb code 7z1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11, PDB code: 7z1n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:58.8 occ:1.00 NE2 A:HIS80 2.1 27.9 1.0 SG A:CYS77 2.3 30.2 1.0 SG A:CYS70 2.3 41.0 1.0 SG A:CYS67 2.3 41.8 1.0 CD2 A:HIS80 2.8 27.9 1.0 CB A:CYS67 2.9 41.8 1.0 CE1 A:HIS80 3.1 27.9 1.0 CB A:CYS77 3.1 30.2 1.0 OG1 A:THR69 3.9 39.5 1.0 CG A:HIS80 3.9 27.9 1.0 CB A:CYS70 4.0 41.0 1.0 ND1 A:HIS80 4.0 27.9 1.0 CA A:CYS77 4.2 30.2 1.0 CA A:CYS67 4.4 41.8 1.0 N A:CYS70 4.4 41.0 1.0 CA A:GLY59 4.4 32.5 1.0 CA A:CYS70 4.7 41.0 1.0 N A:GLY59 5.0 32.5 1.0

Zinc binding site 2 out of 5 in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:61.4 occ:1.00 SG A:CYS110 2.3 31.5 1.0 SG A:CYS157 2.3 42.5 1.0 SG A:CYS154 2.3 43.6 1.0 SG A:CYS107 2.3 28.7 1.0 CB A:CYS154 2.9 43.6 1.0 CB A:CYS107 3.0 28.7 1.0 CB A:CYS110 3.6 31.5 1.0 CB A:CYS157 3.9 42.5 1.0 N A:CYS110 3.9 31.5 1.0 CA A:CYS110 4.3 31.5 1.0 N A:CYS157 4.3 42.5 1.0 CA A:CYS154 4.4 43.6 1.0 CA A:CYS107 4.5 28.7 1.0 CA A:CYS157 4.6 42.5 1.0 O A:CYS157 4.7 42.5 1.0 C A:ASN109 4.8 32.3 1.0 CB A:ASN109 4.8 32.3 1.0 N A:HIS156 4.9 39.8 1.0 CB A:ALA159 4.9 40.8 1.0 C A:HIS156 4.9 39.8 1.0 C A:CYS110 4.9 31.5 1.0 N A:ASN109 5.0 32.3 1.0 C A:CYS157 5.0 42.5 1.0 CB A:HIS156 5.0 39.8 1.0

Zinc binding site 3 out of 5 in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:53.8 occ:1.00 SG B:CYS1098 2.3 23.9 1.0 SG B:CYS1107 2.3 32.0 1.0 SG B:CYS1110 2.3 35.3 1.0 SG B:CYS1095 2.3 27.6 1.0 CB B:CYS1095 3.0 27.6 1.0 CB B:CYS1107 3.4 32.0 1.0 OG1 B:THR1109 3.4 31.8 1.0 CB B:CYS1110 3.7 35.3 1.0 CB B:CYS1098 3.8 23.9 1.0 N B:CYS1110 4.2 35.3 1.0 N B:CYS1098 4.3 23.9 1.0 CA B:CYS1095 4.4 27.6 1.0 CA B:CYS1110 4.6 35.3 1.0 CA B:CYS1098 4.7 23.9 1.0 O B:CYS1095 4.7 27.6 1.0 CB B:THR1109 4.8 31.8 1.0 CA B:CYS1107 4.8 32.0 1.0 C B:CYS1095 4.9 27.6 1.0

Zinc binding site 4 out of 5 in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn100 b:43.9 occ:1.00 SG J:CYS10 2.3 28.4 1.0 SG J:CYS45 2.3 31.7 1.0 SG J:CYS46 2.3 34.0 1.0 SG J:CYS7 2.3 31.0 1.0 CB J:CYS7 2.7 31.0 1.0 N J:CYS46 3.0 34.0 1.0 CB J:CYS10 3.0 28.4 1.0 CB J:CYS45 3.3 31.7 1.0 CA J:CYS46 3.4 34.0 1.0 CB J:CYS46 3.4 34.0 1.0 C J:CYS45 3.4 31.7 1.0 CA J:CYS45 4.0 31.7 1.0 O J:CYS45 4.0 31.7 1.0 N J:CYS10 4.1 28.4 1.0 CA J:CYS10 4.1 28.4 1.0 CA J:CYS7 4.2 31.0 1.0 N J:GLY11 4.5 29.9 1.0 N J:LYS12 4.7 30.6 1.0 CB J:LYS12 4.7 30.6 1.0 N J:CYS45 4.7 31.7 1.0 C J:CYS10 4.9 28.4 1.0 C J:CYS46 4.9 34.0 1.0 C J:CYS7 4.9 31.0 1.0 OG J:SER9 4.9 25.7 1.0 CG J:LYS12 5.0 30.6 1.0

Zinc binding site 5 out of 5 in the Structure of Yeast Rna Polymerase III Delta C53-C37-C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast Rna Polymerase III Delta C53-C37-C11 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:114.6 occ:1.00 SG L:CYS34 2.3 62.3 1.0 SG L:CYS48 2.3 64.0 1.0 SG L:CYS51 2.3 65.5 1.0 SG L:CYS31 2.3 60.3 1.0 CB L:CYS31 3.0 60.3 1.0 CB L:CYS48 3.0 64.0 1.0 CB L:CYS34 3.2 62.3 1.0 CB L:CYS51 4.0 65.5 1.0 N L:CYS51 4.0 65.5 1.0 N L:CYS34 4.2 62.3 1.0 O L:CYS51 4.2 65.5 1.0 CA L:CYS34 4.2 62.3 1.0 CA L:CYS51 4.4 65.5 1.0 CA L:CYS31 4.4 60.3 1.0 CA L:CYS48 4.5 64.0 1.0 C L:CYS51 4.7 65.5 1.0 CB L:ASP50 4.8 65.7 1.0 C L:CYS31 4.9 60.3 1.0 CB L:HIS53 5.0 55.5 1.0

M.Girbig, J.Xie, H.Grotsch, D.Libri, O.Porrua, C.W.Muller. Architecture of the Yeast Pol III Pre-Termination Complex and Pausing Mechanism on Poly(Dt) Termination Signals. Cell Rep V. 40 11316 2022.
ISSN: ESSN 2211-1247
PubMed: 36070694
DOI: 10.1016/J.CELREP.2022.111316