Zinc in PDB 5fj9: Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A

All present enzymatic activity of Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A:
2.7.7.6;

The binding sites of Zinc atom in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A (pdb code 5fj9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A, PDB code: 5fj9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


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 Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:46.8 occ:1.00 NE2 A:HIS80 2.0 94.4 1.0 SG A:CYS77 2.3 0.2 1.0 SG A:CYS67 2.3 0.1 1.0 SG A:CYS70 2.3 0.4 1.0 CD2 A:HIS80 2.9 92.4 1.0 OG1 A:THR69 2.9 1.0 1.0 CE1 A:HIS80 3.1 94.5 1.0 CB A:CYS77 3.2 0.8 1.0 CB A:CYS67 3.5 0.6 1.0 CB A:CYS70 4.1 0.8 1.0 CG A:HIS80 4.1 93.5 1.0 ND1 A:HIS80 4.2 92.4 1.0 N A:CYS70 4.2 0.4 1.0 CA A:CYS77 4.2 0.2 1.0 CB A:THR69 4.2 0.1 1.0 CA A:CYS70 4.6 0.1 1.0 CA A:CYS67 4.9 0.1 1.0 C A:THR69 4.9 0.4 1.0 N A:HIS78 5.0 0.8 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


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 Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.7 occ:1.00 OD1 A:ASN109 2.0 0.8 1.0 SG A:CYS110 2.3 0.9 1.0 SG A:CYS157 2.3 0.2 1.0 SG A:CYS107 2.4 0.7 1.0 SG A:CYS154 2.4 0.0 1.0 CG A:ASN109 3.1 1.0 1.0 CB A:CYS110 3.1 0.6 1.0 N A:CYS110 3.5 0.3 1.0 CB A:CYS107 3.5 0.4 1.0 ND2 A:ASN109 3.6 0.6 1.0 CB A:CYS157 3.9 1.0 1.0 CA A:CYS110 3.9 0.6 1.0 CB A:CYS154 3.9 0.3 1.0 O A:CYS157 4.1 0.6 1.0 O A:CYS107 4.1 0.9 1.0 CB A:ASN109 4.3 0.6 1.0 C A:ASN109 4.6 0.2 1.0 C A:CYS107 4.6 0.3 1.0 O A:ALA159 4.6 0.7 1.0 C A:CYS110 4.6 0.9 1.0 CA A:CYS107 4.6 0.4 1.0 N A:SER111 4.7 0.7 1.0 CA A:ASN109 4.8 0.8 1.0 CA A:CYS157 4.9 0.2 1.0 C A:CYS157 4.9 0.3 1.0 N A:ASN109 4.9 0.5 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


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 Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:51.3 occ:1.00 SG B:CYS1107 2.3 0.1 1.0 SG B:CYS1110 2.3 0.2 1.0 SG B:CYS1098 2.4 0.7 1.0 CB B:CYS1107 3.2 0.6 1.0 SG B:CYS1095 3.5 0.8 1.0 O B:LYS1097 3.6 0.3 1.0 CB B:CYS1095 3.7 0.1 1.0 CB B:CYS1110 3.8 0.8 1.0 CB B:CYS1098 4.2 0.1 1.0 O B:CYS1098 4.2 0.3 1.0 C B:LYS1097 4.5 0.6 1.0 O B:CYS1110 4.5 0.4 1.0 CA B:CYS1107 4.7 0.9 1.0 CA B:CYS1110 4.7 0.0 1.0 O B:CYS1107 4.8 0.3 1.0 N B:CYS1110 4.8 0.9 1.0 C B:CYS1098 4.9 0.9 1.0 CA B:CYS1098 4.9 0.4 1.0 C B:CYS1110 5.0 0.2 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


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 Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2000 b:0.8 occ:1.00 SG I:CYS8 2.3 0.3 1.0 SG I:CYS26 2.3 0.2 1.0 SG I:CYS5 2.4 0.2 1.0 CB I:CYS26 2.4 0.4 1.0 CB I:CYS5 2.6 1.0 1.0 O I:CYS5 3.8 0.0 1.0 CA I:CYS26 3.9 0.3 1.0 CA I:CYS5 3.9 0.8 1.0 CB I:CYS29 4.0 0.0 1.0 SG I:CYS29 4.1 0.9 1.0 CB I:CYS8 4.1 0.4 1.0 C I:CYS5 4.2 0.4 1.0 N I:CYS26 4.6 0.7 1.0 N I:CYS5 4.7 0.1 1.0 O I:PRO6 4.7 0.1 1.0 N I:ASN9 4.7 0.9 1.0 C I:CYS26 4.7 0.8 1.0 CB I:TYR31 4.7 0.1 1.0 CG I:TYR31 4.9 0.7 1.0 OG I:SER7 5.0 0.4 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


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 Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2000 b:31.9 occ:1.00 CB J:CYS10 2.2 78.5 1.0 SG J:CYS10 2.3 79.8 1.0 SG J:CYS7 2.3 72.8 1.0 SG J:CYS45 2.3 94.4 1.0 SG J:CYS46 2.8 96.3 1.0 CB J:CYS7 3.1 72.3 1.0 CB J:CYS45 3.1 93.5 1.0 N J:CYS46 3.3 96.6 1.0 CA J:CYS10 3.4 75.2 1.0 N J:CYS10 3.5 72.8 1.0 C J:CYS45 3.5 90.8 1.0 CA J:CYS46 3.8 98.8 1.0 O J:CYS45 3.9 90.1 1.0 CA J:CYS45 3.9 91.3 1.0 CB J:CYS46 3.9 97.1 1.0 OG J:SER9 4.1 70.3 1.0 N J:GLY11 4.1 81.3 1.0 C J:CYS10 4.2 74.8 1.0 CA J:CYS7 4.5 71.2 1.0 N J:LYS12 4.7 87.8 1.0 C J:SER9 4.7 70.6 1.0 NE J:ARG43 4.7 96.1 1.0 CB J:LYS12 4.8 93.0 1.0 C J:CYS7 4.9 70.8 1.0 N J:CYS45 4.9 91.3 1.0 NH2 J:ARG43 5.0 0.1 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Yeast Apo Rna Polymerase III at 4.6 A within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn2000 b:27.9 occ:1.00 CB L:CYS51 2.0 0.3 1.0 SG L:CYS51 2.1 0.6 1.0 CB L:CYS48 2.1 0.7 1.0 SG L:CYS48 2.2 0.5 1.0 SG L:CYS34 2.3 0.1 1.0 SG L:CYS31 2.4 0.9 1.0 CB L:CYS34 3.0 0.6 1.0 CA L:CYS51 3.3 0.2 1.0 CB L:CYS31 3.5 0.8 1.0 CA L:CYS48 3.6 0.3 1.0 N L:LYS49 4.1 0.7 1.0 C L:CYS48 4.2 0.7 1.0 N L:CYS51 4.2 0.8 1.0 C L:CYS51 4.2 0.3 1.0 N L:CYS48 4.3 0.6 1.0 O L:CYS51 4.4 0.7 1.0 CA L:CYS34 4.5 0.6 1.0 CA L:CYS31 4.5 0.6 1.0 O L:HIS53 4.6 0.6 1.0 OD1 L:ASP50 4.8 0.3 1.0 N L:CYS34 4.8 0.1 1.0

N.A.Hoffmann, A.J.Jakobi, M.Moreno-Morcillo, S.Glatt, J.Kosinski, W.J.H.Hagen, C.Sachse, C.W.Muller. Molecular Structures of Unbound and Transcribing Rna Polymerase III. Nature V. 528 231 2015.
ISSN: ISSN 0028-0836
PubMed: 26605533
DOI: 10.1038/NATURE16143