Zinc in PDB 6eu1: Rna Polymerase III - Open Dna Complex (Oc-POL3)

All present enzymatic activity of Rna Polymerase III - Open Dna Complex (Oc-POL3):
2.7.7.6;

The structure of Rna Polymerase III - Open Dna Complex (Oc-POL3) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Rna Polymerase III - Open Dna Complex (Oc-POL3) (pdb code 6eu1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rna Polymerase III - Open Dna Complex (Oc-POL3), PDB code: 6eu1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:23.1 occ:1.00 CB A:CYS70 2.6 28.0 1.0 SG A:CYS77 3.0 23.9 1.0 SG A:CYS67 3.1 29.5 1.0 CB A:CYS77 3.2 23.9 1.0 SG A:CYS70 3.3 28.0 1.0 NE2 A:HIS80 3.3 13.6 1.0 O A:CYS70 3.4 28.0 1.0 CA A:CYS70 3.5 28.0 1.0 CB A:CYS67 3.5 29.5 1.0 N A:CYS70 3.5 28.0 1.0 CD2 A:HIS80 3.5 13.6 1.0 CA A:GLY59 3.8 25.0 1.0 C A:CYS70 3.9 28.0 1.0 CA A:CYS77 4.0 23.9 1.0 OG1 A:THR69 4.0 23.2 1.0 N A:GLY59 4.3 25.0 1.0 N A:HIS78 4.6 17.8 1.0 CE1 A:HIS80 4.6 13.6 1.0 C A:CYS77 4.7 23.9 1.0 C A:THR69 4.8 23.2 1.0 C A:GLY59 4.8 25.0 1.0 CG A:HIS80 4.8 13.6 1.0 N A:GLY79 4.9 16.9 1.0 CA A:CYS67 5.0 29.5 1.0

Zinc binding site 2 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:20.1 occ:1.00 SG A:CYS107 2.6 15.9 1.0 CB A:CYS107 2.9 15.9 1.0 CB A:CYS154 3.1 27.4 1.0 CB A:CYS157 3.1 28.4 1.0 CB A:CYS110 3.6 18.6 1.0 SG A:CYS154 3.9 27.4 1.0 N A:CYS110 4.0 18.6 1.0 SG A:CYS157 4.0 28.4 1.0 CA A:CYS110 4.3 18.6 1.0 CA A:CYS107 4.4 15.9 1.0 CA A:CYS157 4.4 28.4 1.0 CA A:CYS154 4.4 27.4 1.0 N A:CYS157 4.4 28.4 1.0 N A:SER111 4.7 15.6 1.0 CB A:ALA159 4.7 21.0 1.0 N A:LEU155 4.7 28.1 1.0 SG A:CYS110 4.8 18.6 1.0 C A:CYS110 4.9 18.6 1.0 N A:ALA112 4.9 14.0 1.0

Zinc binding site 3 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:35.7 occ:1.00 SG B:CYS1110 2.6 22.9 1.0 SG B:CYS1095 3.2 13.2 1.0 O B:CYS1098 3.3 14.6 1.0 CB B:CYS1095 3.3 13.2 1.0 O B:LYS1097 3.4 11.0 1.0 SG B:CYS1098 3.4 14.6 1.0 CG2 B:THR1109 3.8 17.1 1.0 CB B:CYS1107 4.1 24.5 1.0 CB B:CYS1110 4.1 22.9 1.0 C B:CYS1098 4.1 14.6 1.0 SG B:CYS1107 4.4 24.5 1.0 N B:CYS1110 4.4 22.9 1.0 N B:LEU1100 4.5 8.9 1.0 C B:LYS1097 4.6 11.0 1.0 CB B:CYS1098 4.6 14.6 1.0 O B:CYS1107 4.7 24.5 1.0 CA B:CYS1095 4.8 13.2 1.0 CA B:CYS1098 4.8 14.6 1.0 CA B:CYS1110 4.9 22.9 1.0 CA B:CYS1107 4.9 24.5 1.0 N B:GLY1099 5.0 11.0 1.0

Zinc binding site 4 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:56.2 occ:1.00 CB I:CYS29 2.5 47.1 1.0 SG I:CYS5 2.5 34.1 1.0 CB I:ASN10 2.9 37.2 1.0 N I:ASN10 2.9 37.2 1.0 O I:CYS8 3.0 39.5 1.0 SG I:CYS8 3.1 39.5 1.0 C I:CYS8 3.1 39.5 1.0 SG I:CYS29 3.3 47.1 1.0 N I:ASN9 3.3 39.3 1.0 CA I:ASN10 3.4 37.2 1.0 C I:ASN9 3.4 39.3 1.0 CB I:CYS8 3.5 39.5 1.0 CA I:CYS29 3.9 47.1 1.0 CA I:CYS8 3.9 39.5 1.0 CA I:ASN9 4.0 39.3 1.0 CB I:CYS5 4.0 34.1 1.0 O I:ASN9 4.1 39.3 1.0 C I:ASN10 4.2 37.2 1.0 CG I:ASN10 4.3 37.2 1.0 O I:SER28 4.5 40.4 1.0 O I:ASN10 4.6 37.2 1.0 ND2 I:ASN10 4.6 37.2 1.0 N I:CYS8 4.7 39.5 1.0 N I:CYS29 4.7 47.1 1.0 C I:CYS29 4.9 47.1 1.0 N I:MET11 4.9 40.3 1.0 C I:SER28 4.9 40.4 1.0 O I:CYS29 5.0 47.1 1.0

Zinc binding site 5 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:21.1 occ:1.00 SG J:CYS46 2.5 5.9 1.0 CB J:CYS10 2.6 21.1 1.0 N J:CYS46 3.1 5.9 1.0 C J:CYS45 3.3 7.5 1.0 CB J:CYS7 3.3 14.0 1.0 CA J:CYS46 3.4 5.9 1.0 CB J:CYS45 3.4 7.5 1.0 N J:CYS10 3.5 21.1 1.0 CB J:CYS46 3.5 5.9 1.0 O J:CYS45 3.6 7.5 1.0 CA J:CYS10 3.6 21.1 1.0 SG J:CYS7 3.6 14.0 1.0 SG J:CYS10 3.9 21.1 1.0 CA J:CYS45 4.0 7.5 1.0 OG J:SER9 4.0 12.3 1.0 N J:GLY11 4.3 21.1 1.0 C J:CYS10 4.5 21.1 1.0 C J:SER9 4.7 12.3 1.0 CA J:CYS7 4.8 14.0 1.0 N J:CYS45 4.8 7.5 1.0 CG J:ARG43 4.8 8.0 1.0 C J:CYS46 4.9 5.9 1.0 CD J:ARG43 4.9 8.0 1.0

Zinc binding site 6 out of 6 in the Rna Polymerase III - Open Dna Complex (Oc-POL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase III - Open Dna Complex (Oc-POL3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:27.1 occ:1.00 SG L:CYS31 2.6 10.6 1.0 SG L:CYS48 2.7 16.9 1.0 SG L:CYS51 2.9 16.5 1.0 CB L:CYS48 3.1 16.9 1.0 CB L:CYS34 3.2 23.2 1.0 SG L:CYS34 3.3 23.2 1.0 CB L:CYS31 3.5 10.6 1.0 N L:CYS34 3.5 23.2 1.0 CA L:CYS34 3.9 23.2 1.0 CB L:HIS53 4.1 13.8 1.0 OG L:SER36 4.2 15.0 1.0 CB L:CYS51 4.3 16.5 1.0 OE1 L:GLU33 4.5 21.0 1.0 N L:CYS51 4.7 16.5 1.0 CA L:CYS48 4.7 16.9 1.0 C L:GLU33 4.7 21.0 1.0 N L:HIS53 4.8 13.8 1.0 C L:CYS34 4.8 23.2 1.0 CB L:GLU33 4.8 21.0 1.0 N L:GLU33 4.8 21.0 1.0 CA L:CYS31 4.9 10.6 1.0 N L:SER35 4.9 19.6 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