Zinc in PDB 6eu3: Apo Rna Polymerase III - Closed Conformation (CPOL3)

All present enzymatic activity of Apo Rna Polymerase III - Closed Conformation (CPOL3):
2.7.7.6;

The structure of Apo Rna Polymerase III - Closed Conformation (CPOL3) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Apo Rna Polymerase III - Closed Conformation (CPOL3) (pdb code 6eu3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Apo Rna Polymerase III - Closed Conformation (CPOL3), PDB code: 6eu3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:67.2 occ:1.00 SG A:CYS70 2.5 63.7 1.0 SG A:CYS67 2.5 71.8 1.0 SG A:CYS77 3.0 54.6 1.0 CE1 A:HIS80 3.1 36.1 1.0 CB A:CYS67 3.2 71.8 1.0 CB A:CYS77 3.2 54.6 1.0 ND1 A:HIS80 3.4 36.1 1.0 OG1 A:THR69 3.9 63.9 1.0 CA A:CYS77 4.1 54.6 1.0 O A:CYS70 4.1 63.7 1.0 CB A:CYS70 4.2 63.7 1.0 NE2 A:HIS80 4.3 36.1 1.0 O A:MET58 4.3 42.7 1.0 N A:CYS70 4.4 63.7 1.0 CA A:GLY59 4.5 50.3 1.0 CA A:CYS70 4.7 63.7 1.0 CG A:HIS80 4.7 36.1 1.0 CA A:CYS67 4.7 71.8 1.0 C A:CYS77 4.7 54.6 1.0 N A:GLY79 4.8 39.5 1.0 N A:HIS78 4.8 42.6 1.0 C A:CYS70 4.9 63.7 1.0 C A:MET58 5.0 42.7 1.0

Zinc binding site 2 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.4 occ:1.00 SG A:CYS107 2.5 41.0 1.0 SG A:CYS157 2.5 54.9 1.0 SG A:CYS154 2.5 63.7 1.0 CB A:CYS110 2.6 43.2 1.0 CB A:CYS107 3.0 41.0 1.0 N A:CYS110 3.5 43.2 1.0 CB A:CYS154 3.5 63.7 1.0 CA A:CYS110 3.6 43.2 1.0 CB A:CYS157 3.8 54.9 1.0 SG A:CYS110 3.9 43.2 1.0 N A:CYS157 4.2 54.9 1.0 CA A:CYS107 4.4 41.0 1.0 C A:CYS110 4.5 43.2 1.0 CA A:CYS157 4.6 54.9 1.0 C A:ASN109 4.7 40.8 1.0 N A:SER111 4.8 36.4 1.0 C A:CYS107 4.8 41.0 1.0 C A:HIS156 4.8 53.8 1.0 N A:HIS156 4.8 53.8 1.0 CB A:HIS156 4.9 53.8 1.0 O A:CYS107 5.0 41.0 1.0 N A:ASN109 5.0 40.8 1.0 CA A:CYS154 5.0 63.7 1.0 CB A:ASN109 5.0 40.8 1.0

Zinc binding site 3 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:41.1 occ:1.00 SG B:CYS1095 2.5 27.4 1.0 SG B:CYS1107 2.5 47.1 1.0 O B:LYS1097 2.6 29.3 1.0 SG B:CYS1098 2.8 25.2 1.0 O B:CYS1098 3.0 25.2 1.0 CB B:CYS1095 3.6 27.4 1.0 C B:CYS1098 3.7 25.2 1.0 CB B:CYS1110 3.7 56.4 1.0 C B:LYS1097 3.8 29.3 1.0 CB B:CYS1098 4.0 25.2 1.0 CA B:CYS1098 4.2 25.2 1.0 CB B:CYS1107 4.2 47.1 1.0 N B:CYS1110 4.3 56.4 1.0 N B:CYS1098 4.4 25.2 1.0 CA B:CYS1110 4.7 56.4 1.0 N B:GLY1099 4.7 19.6 1.0 N B:LEU1100 4.7 20.4 1.0 CB B:THR1109 4.9 45.9 1.0 CA B:CYS1095 5.0 27.4 1.0 CA B:LYS1097 5.0 29.3 1.0 CA B:GLY1099 5.0 19.6 1.0

Zinc binding site 4 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:92.4 occ:1.00 N I:SER7 2.3 75.6 1.0 N I:CYS8 2.5 74.5 1.0 CB I:CYS5 2.6 78.9 1.0 CA I:SER7 2.8 75.6 1.0 C I:CYS5 2.9 78.9 1.0 CB I:SER7 3.0 75.6 1.0 C I:SER7 3.0 75.6 1.0 N I:PRO6 3.2 72.1 1.0 O I:CYS5 3.2 78.9 1.0 CA I:CYS5 3.2 78.9 1.0 C I:PRO6 3.3 72.1 1.0 SG I:CYS8 3.4 74.5 1.0 SG I:CYS29 3.6 81.7 1.0 CA I:CYS8 3.7 74.5 1.0 CA I:PRO6 3.8 72.1 1.0 CB I:CYS8 3.9 74.5 1.0 SG I:CYS5 4.0 78.9 1.0 CD I:PRO6 4.0 72.1 1.0 N I:ASN9 4.0 69.5 1.0 OG I:SER7 4.2 75.6 1.0 O I:SER7 4.2 75.6 1.0 C I:CYS8 4.3 74.5 1.0 O I:PRO6 4.4 72.1 1.0 N I:CYS5 4.5 78.9 1.0 CB I:PRO6 4.8 72.1 1.0 CG I:TYR31 4.9 84.8 1.0 CD1 I:TYR31 5.0 84.8 1.0

Zinc binding site 5 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:55.3 occ:1.00 SG J:CYS46 2.5 18.9 1.0 SG J:CYS45 2.5 22.0 1.0 SG J:CYS10 2.5 24.2 1.0 NH2 J:ARG43 3.0 25.6 1.0 CZ J:ARG43 3.4 25.6 1.0 CB J:CYS45 3.5 22.0 1.0 CB J:CYS10 3.5 24.2 1.0 NH1 J:ARG43 3.8 25.6 1.0 N J:CYS10 3.9 24.2 1.0 C J:CYS45 3.9 22.0 1.0 N J:CYS46 3.9 18.9 1.0 CB J:CYS46 3.9 18.9 1.0 SG J:CYS7 4.1 19.3 1.0 NE J:ARG43 4.2 25.6 1.0 O J:CYS45 4.2 22.0 1.0 CA J:CYS10 4.3 24.2 1.0 CA J:CYS45 4.3 22.0 1.0 CA J:CYS46 4.4 18.9 1.0 CB J:SER9 4.5 22.2 1.0 CB J:CYS7 4.6 19.3 1.0 N J:GLY11 4.9 17.8 1.0 C J:SER9 4.9 22.2 1.0 CG1 B:ILE938 5.0 19.8 1.0

Zinc binding site 6 out of 6 in the Apo Rna Polymerase III - Closed Conformation (CPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apo Rna Polymerase III - Closed Conformation (CPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:54.3 occ:1.00 SG L:CYS51 2.5 48.7 1.0 SG L:CYS31 2.7 31.2 1.0 SG L:CYS48 2.7 49.6 1.0 SG L:CYS34 2.8 37.9 1.0 CB L:CYS48 2.8 49.6 1.0 CB L:CYS31 3.2 31.2 1.0 CB L:CYS51 3.9 48.7 1.0 OG L:SER36 4.0 43.1 1.0 N L:CYS51 4.0 48.7 1.0 CA L:CYS48 4.3 49.6 1.0 CB L:CYS34 4.3 37.9 1.0 CB L:HIS53 4.4 34.0 1.0 N L:GLY52 4.5 36.5 1.0 N L:HIS53 4.5 34.0 1.0 CA L:CYS51 4.5 48.7 1.0 CB L:ASP50 4.6 59.5 1.0 CA L:CYS31 4.6 31.2 1.0 N L:CYS34 4.7 37.9 1.0 N L:ASP50 4.9 59.5 1.0 C L:CYS48 4.9 49.6 1.0 C L:ASP50 5.0 59.5 1.0

G.Abascal-Palacios, E.P.Ramsay, F.Beuron, E.Morris, A.Vannini. Structural Basis of Rna Polymerase III Transcription Initiation. Nature V. 553 301 2018.
ISSN: ESSN 1476-4687
PubMed: 29345637
DOI: 10.1038/NATURE25441