Zinc in PDB 5fj8: Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 A

All present enzymatic activity of Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 A:
2.7.7.6;

The binding sites of Zinc atom in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 A (pdb code 5fj8). 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 Rna Polymerase III Elongation Complex at 3. 9 A, PDB code: 5fj8:
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 Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:55.6 occ:1.00 NE2 A:HIS80 2.1 50.9 1.0 SG A:CYS77 2.3 53.9 1.0 SG A:CYS70 2.4 69.7 1.0 SG A:CYS67 2.4 69.6 1.0 CD2 A:HIS80 2.9 51.3 1.0 OG1 A:THR69 3.0 66.5 1.0 CE1 A:HIS80 3.2 51.4 1.0 CB A:CYS77 3.2 55.1 1.0 CB A:CYS67 3.5 69.9 1.0 CG A:HIS80 4.1 51.5 1.0 CA A:CYS77 4.2 56.6 1.0 CB A:CYS70 4.2 69.0 1.0 ND1 A:HIS80 4.2 52.6 1.0 N A:CYS70 4.3 68.0 1.0 CB A:THR69 4.4 67.5 1.0 CA A:CYS70 4.7 68.7 1.0 N A:HIS78 5.0 56.9 1.0 CA A:CYS67 5.0 69.9 1.0 O A:CYS70 5.0 68.3 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:25.8 occ:1.00 OD1 A:ASN109 2.1 72.8 1.0 SG A:CYS110 2.3 71.4 1.0 SG A:CYS157 2.3 78.5 1.0 SG A:CYS154 2.4 70.3 1.0 SG A:CYS107 2.5 67.7 1.0 CG A:ASN109 3.1 73.4 1.0 CB A:CYS110 3.1 69.4 1.0 ND2 A:ASN109 3.5 75.0 1.0 N A:CYS110 3.6 68.7 1.0 CB A:CYS157 3.7 77.0 1.0 O A:CYS157 3.8 75.9 1.0 CB A:CYS154 3.9 70.4 1.0 CB A:CYS107 3.9 66.2 1.0 CA A:CYS110 4.0 68.8 1.0 CB A:ASN109 4.4 71.8 1.0 O A:ALA159 4.4 77.1 1.0 C A:CYS157 4.6 76.7 1.0 CA A:CYS157 4.6 76.2 1.0 C A:ASN109 4.7 68.8 1.0 C A:CYS110 4.8 67.7 1.0 O A:CYS107 4.8 63.3 1.0 N A:SER111 4.9 66.5 1.0 CA A:ASN109 5.0 69.2 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:39.4 occ:1.00 SG B:CYS1110 2.3 64.0 1.0 SG B:CYS1107 2.3 60.2 1.0 SG B:CYS1098 2.4 61.0 1.0 CB B:CYS1107 3.3 60.5 1.0 SG B:CYS1095 3.5 64.2 1.0 O B:LYS1097 3.6 64.1 1.0 CB B:CYS1095 3.6 63.4 1.0 CB B:CYS1110 3.9 63.5 1.0 CB B:CYS1098 4.2 61.3 1.0 O B:CYS1098 4.2 58.9 1.0 C B:LYS1097 4.5 63.8 1.0 O B:CYS1110 4.5 63.2 1.0 CA B:CYS1107 4.7 60.5 1.0 O B:CYS1107 4.7 60.6 1.0 N B:CYS1110 4.8 63.6 1.0 CA B:CYS1110 4.8 63.3 1.0 C B:CYS1098 4.9 59.6 1.0 CA B:CYS1098 5.0 60.7 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2000 b:0.2 occ:1.00 CB I:CYS5 2.3 71.7 1.0 SG I:CYS8 2.4 71.3 1.0 SG I:CYS26 2.4 68.4 1.0 SG I:CYS5 2.4 73.2 1.0 CB I:CYS26 2.6 68.9 1.0 SG I:CYS29 3.0 70.2 1.0 CA I:CYS5 3.8 71.0 1.0 CA I:CYS26 4.1 68.8 1.0 CB I:CYS8 4.2 71.8 1.0 O I:PRO6 4.3 69.1 1.0 C I:CYS5 4.3 69.8 1.0 N I:CYS5 4.4 70.5 1.0 O I:CYS5 4.5 68.2 1.0 N I:ASN9 4.5 72.2 1.0 CB I:CYS29 4.7 69.7 1.0 C I:CYS26 4.8 68.4 1.0 N I:CYS26 4.9 69.7 1.0 N I:ASN10 4.9 71.8 1.0 CB I:TYR31 4.9 68.7 1.0 CD2 I:LEU12 5.0 70.4 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2000 b:13.0 occ:1.00 CB J:CYS10 2.1 49.4 1.0 SG J:CYS10 2.3 48.8 1.0 SG J:CYS45 2.3 55.6 1.0 SG J:CYS7 2.4 43.5 1.0 CB J:CYS45 3.1 55.1 1.0 SG J:CYS46 3.1 51.0 1.0 CA J:CYS10 3.2 48.8 1.0 N J:CYS10 3.3 48.5 1.0 CB J:CYS7 3.4 43.4 1.0 OG J:SER9 3.7 47.2 1.0 N J:CYS46 3.7 53.5 1.0 C J:CYS45 3.8 56.0 1.0 N J:GLY11 4.0 51.0 1.0 CA J:CYS45 4.1 55.8 1.0 C J:CYS10 4.1 48.7 1.0 CA J:CYS46 4.3 52.0 1.0 O J:CYS45 4.3 56.6 1.0 CB J:CYS46 4.4 50.8 1.0 C J:SER9 4.5 47.4 1.0 NE J:ARG43 4.6 53.5 1.0 N J:LYS12 4.7 53.5 1.0 CA J:CYS7 4.8 43.3 1.0 NH2 J:ARG43 4.8 55.6 1.0 CB J:LYS12 4.9 60.9 1.0 CB J:SER9 4.9 47.3 1.0 CG J:LYS12 5.0 62.8 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Yeast Rna Polymerase III Elongation Complex at 3. 9 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 Rna Polymerase III Elongation Complex at 3. 9 A within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn2000 b:0.7 occ:1.00 SG L:CYS51 2.0 76.6 1.0 CB L:CYS51 2.1 76.6 1.0 CB L:CYS48 2.1 71.5 1.0 SG L:CYS48 2.2 72.0 1.0 SG L:CYS34 2.3 73.0 1.0 SG L:CYS31 2.5 68.4 1.0 CB L:CYS34 3.2 73.0 1.0 CB L:CYS31 3.3 69.0 1.0 CA L:CYS51 3.3 76.1 1.0 CA L:CYS48 3.6 69.6 1.0 N L:LYS49 4.0 73.1 1.0 C L:CYS48 4.1 69.0 1.0 N L:CYS51 4.1 76.4 1.0 C L:CYS51 4.3 75.8 1.0 N L:CYS48 4.4 69.8 1.0 CA L:CYS31 4.4 69.9 1.0 O L:CYS51 4.5 76.0 1.0 CA L:CYS34 4.6 73.3 1.0 OD1 L:ASP50 4.7 77.4 1.0 O L:HIS53 4.7 72.9 1.0 N L:CYS34 4.9 71.8 1.0 C L:ASP50 5.0 80.1 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