Zinc in PDB 6eu2: Apo Rna Polymerase III - Open Conformation (OPOL3)

All present enzymatic activity of Apo Rna Polymerase III - Open Conformation (OPOL3):
2.7.7.6;

The structure of Apo Rna Polymerase III - Open Conformation (OPOL3) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Apo Rna Polymerase III - Open Conformation (OPOL3) (pdb code 6eu2). 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 - Open Conformation (OPOL3), PDB code: 6eu2:
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 - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:82.1 occ:1.00 CE1 A:HIS80 2.4 45.2 1.0 SG A:CYS70 2.5 66.9 1.0 ND1 A:HIS80 2.9 45.2 1.0 SG A:CYS67 3.1 67.2 1.0 NE2 A:HIS80 3.6 45.2 1.0 SG A:CYS77 3.6 66.2 1.0 CB A:CYS77 3.6 66.2 1.0 OG1 A:THR69 3.7 64.4 1.0 CB A:CYS67 3.9 67.2 1.0 CB A:CYS70 4.2 66.9 1.0 CG A:HIS80 4.3 45.2 1.0 CA A:CYS77 4.3 66.2 1.0 O A:CYS70 4.3 66.9 1.0 N A:CYS70 4.4 66.9 1.0 CD2 A:HIS80 4.6 45.2 1.0 N A:GLY79 4.6 45.4 1.0 CA A:GLY59 4.6 56.5 1.0 N A:HIS78 4.7 46.8 1.0 CA A:CYS70 4.7 66.9 1.0 C A:CYS77 4.8 66.2 1.0 O A:MET58 5.0 57.0 1.0 C A:CYS70 5.0 66.9 1.0

Zinc binding site 2 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:82.4 occ:1.00 SG A:CYS154 2.5 68.3 1.0 SG A:CYS157 2.5 70.2 1.0 SG A:CYS107 2.5 48.5 1.0 CB A:CYS110 2.6 53.6 1.0 N A:CYS110 3.1 53.6 1.0 CB A:CYS107 3.2 48.5 1.0 CB A:CYS154 3.3 68.3 1.0 CA A:CYS110 3.4 53.6 1.0 CB A:CYS157 3.9 70.2 1.0 SG A:CYS110 4.1 53.6 1.0 C A:ASN109 4.2 54.5 1.0 N A:CYS157 4.2 70.2 1.0 CB A:ASN109 4.3 54.5 1.0 C A:CYS110 4.3 53.6 1.0 N A:SER111 4.5 44.2 1.0 N A:ASN109 4.6 54.5 1.0 CA A:ASN109 4.6 54.5 1.0 CA A:CYS157 4.6 70.2 1.0 CA A:CYS107 4.6 48.5 1.0 CA A:CYS154 4.8 68.3 1.0 CB A:HIS156 4.9 67.0 1.0 C A:HIS156 4.9 67.0 1.0 C A:CYS107 5.0 48.5 1.0

Zinc binding site 3 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:97.5 occ:1.00 O B:LYS1097 2.5 36.6 1.0 SG B:CYS1107 2.5 46.2 1.0 SG B:CYS1095 2.5 37.6 1.0 SG B:CYS1098 3.3 39.3 1.0 CB B:CYS1095 3.3 37.6 1.0 O B:CYS1098 3.6 39.3 1.0 C B:LYS1097 3.7 36.6 1.0 CB B:CYS1110 4.1 55.5 1.0 CB B:CYS1107 4.1 46.2 1.0 C B:CYS1098 4.2 39.3 1.0 CB B:CYS1098 4.5 39.3 1.0 N B:CYS1098 4.5 39.3 1.0 CA B:CYS1098 4.6 39.3 1.0 N B:CYS1110 4.7 55.5 1.0 CA B:LYS1097 4.7 36.6 1.0 CA B:CYS1095 4.7 37.6 1.0 N B:LYS1097 4.8 36.6 1.0 CB B:LYS1097 4.8 36.6 1.0

Zinc binding site 4 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.3 occ:1.00 SG I:CYS29 2.5 90.9 1.0 SG I:CYS8 2.5 81.5 1.0 CB I:CYS5 2.5 84.8 1.0 N I:CYS8 3.1 81.5 1.0 SG I:CYS5 3.1 84.8 1.0 CB I:CYS8 3.5 81.5 1.0 CA I:CYS8 3.8 81.5 1.0 CB I:SER7 3.8 81.1 1.0 CA I:CYS5 3.8 84.8 1.0 N I:SER7 3.9 81.1 1.0 C I:SER7 3.9 81.1 1.0 CB I:CYS29 3.9 90.9 1.0 CA I:SER7 4.0 81.1 1.0 C I:CYS5 4.2 84.8 1.0 SG I:CYS26 4.3 88.2 1.0 N I:ASN9 4.3 70.7 1.0 C I:CYS8 4.4 81.5 1.0 OG I:SER7 4.6 81.1 1.0 O I:CYS5 4.6 84.8 1.0 N I:PRO6 4.7 77.0 1.0 CB I:TYR31 4.8 87.8 1.0 N I:ASN10 4.9 70.6 1.0 CB I:SER28 4.9 90.2 1.0 N I:CYS5 5.0 84.8 1.0 O I:SER7 5.0 81.1 1.0

Zinc binding site 5 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:53.0 occ:1.00 SG J:CYS45 2.5 29.1 1.0 SG J:CYS10 2.5 24.1 1.0 SG J:CYS46 2.5 23.9 1.0 CB J:CYS10 3.3 24.1 1.0 N J:CYS10 3.3 24.1 1.0 NH2 J:ARG43 3.6 27.1 1.0 SG J:CYS7 3.7 27.5 1.0 CB J:CYS45 3.7 29.1 1.0 CA J:CYS10 3.9 24.1 1.0 NH1 J:ARG43 3.9 27.1 1.0 CZ J:ARG43 3.9 27.1 1.0 CB J:CYS46 4.1 23.9 1.0 CB J:SER9 4.1 23.1 1.0 N J:CYS46 4.1 23.9 1.0 C J:CYS45 4.2 29.1 1.0 CB J:CYS7 4.2 27.5 1.0 N J:GLY11 4.4 24.3 1.0 C J:SER9 4.4 23.1 1.0 CA J:CYS45 4.6 29.1 1.0 CA J:CYS46 4.6 23.9 1.0 O J:CYS45 4.6 29.1 1.0 CA J:SER9 4.6 23.1 1.0 N J:SER9 4.6 23.1 1.0 C J:CYS10 4.6 24.1 1.0 NE J:ARG43 4.8 27.1 1.0

Zinc binding site 6 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


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 - Open Conformation (OPOL3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.6 occ:1.00 SG L:CYS51 2.5 62.4 1.0 SG L:CYS34 2.5 58.4 1.0 SG L:CYS31 2.5 46.9 1.0 CB L:CYS31 2.9 46.9 1.0 SG L:CYS48 3.0 64.0 1.0 CB L:CYS48 3.1 64.0 1.0 CB L:CYS51 3.8 62.4 1.0 N L:CYS51 4.0 62.4 1.0 CB L:CYS34 4.0 58.4 1.0 OG L:SER36 4.0 53.5 1.0 N L:CYS34 4.4 58.4 1.0 CA L:CYS31 4.4 46.9 1.0 CA L:CYS51 4.4 62.4 1.0 CA L:CYS48 4.5 64.0 1.0 N L:GLY52 4.6 50.6 1.0 CB L:ASP50 4.7 69.3 1.0 CB L:HIS53 4.7 45.1 1.0 CA L:CYS34 4.7 58.4 1.0 N L:HIS53 4.8 45.1 1.0 CD2 L:LEU38 4.8 57.3 1.0 N L:ASP50 5.0 69.3 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