Zinc in PDB 6cnf: Yeast Rna Polymerase III Elongation Complex

All present enzymatic activity of Yeast Rna Polymerase III Elongation Complex:
2.7.7.6;

The binding sites of Zinc atom in the Yeast Rna Polymerase III Elongation Complex (pdb code 6cnf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Yeast Rna Polymerase III Elongation Complex, PDB code: 6cnf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:0.0 occ:1.00 NE2 A:HIS80 1.9 0.0 1.0 SG A:CYS67 2.4 0.0 1.0 SG A:CYS70 2.5 0.0 1.0 SG A:CYS77 2.6 0.0 1.0 N A:CYS70 2.7 0.0 1.0 CD2 A:HIS80 2.8 0.0 1.0 OG1 A:THR69 2.8 0.0 1.0 CE1 A:HIS80 3.0 0.0 1.0 CB A:CYS70 3.1 0.0 1.0 CB A:CYS67 3.2 0.0 1.0 CA A:CYS70 3.2 0.0 1.0 O A:CYS70 3.3 0.0 1.0 C A:CYS70 3.7 0.0 1.0 C A:THR69 3.8 0.0 1.0 CB A:THR69 3.9 0.0 1.0 CB A:CYS77 3.9 0.0 1.0 CG A:HIS80 4.0 0.0 1.0 ND1 A:HIS80 4.0 0.0 1.0 O A:CYS67 4.1 0.0 1.0 CA A:THR69 4.4 0.0 1.0 CA A:CYS67 4.5 0.0 1.0 C A:CYS67 4.6 0.0 1.0 O A:LYS57 4.7 0.0 1.0 N A:THR69 4.7 0.0 1.0 O A:THR69 4.8 0.0 1.0 CA A:CYS77 4.8 0.0 1.0 N A:HIS71 4.9 0.0 1.0

Zinc binding site 2 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:0.0 occ:1.00 OD1 A:ASN109 2.1 0.0 1.0 SG A:CYS110 2.3 0.0 1.0 SG A:CYS154 2.3 0.0 1.0 SG A:CYS157 2.4 0.0 1.0 SG A:CYS107 2.4 0.0 1.0 CB A:CYS157 2.7 0.0 1.0 CB A:CYS154 2.8 0.0 1.0 CG A:ASN109 3.0 0.0 1.0 ND2 A:ASN109 3.2 0.0 1.0 CB A:CYS107 3.5 0.0 1.0 N A:CYS110 3.7 0.0 1.0 CB A:CYS110 3.7 0.0 1.0 CA A:CYS157 3.9 0.0 1.0 N A:CYS157 4.1 0.0 1.0 N A:SER111 4.1 0.0 1.0 CA A:CYS110 4.1 0.0 1.0 CA A:CYS154 4.2 0.0 1.0 N A:ALA112 4.3 0.0 1.0 C A:CYS110 4.3 0.0 1.0 CB A:ASN109 4.4 0.0 1.0 N A:LEU155 4.5 0.0 1.0 C A:CYS154 4.7 0.0 1.0 C A:ASN109 4.8 0.0 1.0 CB A:ALA112 4.8 0.0 1.0 CA A:CYS107 4.9 0.0 1.0 O A:ALA112 4.9 0.0 1.0 CA A:SER111 4.9 0.0 1.0 N A:ASN109 4.9 0.0 1.0 C A:CYS157 4.9 0.0 1.0 CA A:ASN109 4.9 0.0 1.0

Zinc binding site 3 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:0.0 occ:1.00 O B:LYS1097 2.3 0.0 1.0 SG B:CYS1107 2.4 0.0 1.0 CB B:CYS1095 2.5 0.0 1.0 SG B:CYS1110 2.5 0.0 1.0 SG B:CYS1095 2.6 0.0 1.0 SG B:CYS1098 2.6 0.0 1.0 O B:CYS1098 2.8 0.0 1.0 C B:LYS1097 3.4 0.0 1.0 C B:CYS1098 3.6 0.0 1.0 CA B:CYS1095 3.8 0.0 1.0 O B:CYS1095 3.8 0.0 1.0 CB B:CYS1098 3.9 0.0 1.0 CB B:CYS1107 3.9 0.0 1.0 C B:CYS1095 4.0 0.0 1.0 CA B:CYS1098 4.1 0.0 1.0 N B:CYS1098 4.1 0.0 1.0 CB B:CYS1110 4.2 0.0 1.0 CA B:LYS1097 4.5 0.0 1.0 N B:CYS1095 4.5 0.0 1.0 N B:GLY1099 4.6 0.0 1.0 CB B:LYS1097 4.6 0.0 1.0 N B:LYS1097 4.8 0.0 1.0 N B:LEU1100 4.8 0.0 1.0 CA B:GLY1099 4.9 0.0 1.0

Zinc binding site 4 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2000 b:0.0 occ:1.00 CB I:CYS26 2.3 0.0 1.0 SG I:CYS26 2.3 0.0 1.0 O I:CYS29 2.4 0.0 1.0 SG I:CYS8 2.6 0.0 1.0 SG I:CYS5 2.6 0.0 1.0 CB I:CYS8 2.7 0.0 1.0 SG I:CYS29 2.7 0.0 1.0 C I:CYS29 3.2 0.0 1.0 CB I:CYS29 3.5 0.0 1.0 CA I:CYS26 3.7 0.0 1.0 CA I:CYS29 3.9 0.0 1.0 O I:CYS26 3.9 0.0 1.0 C I:CYS26 3.9 0.0 1.0 C I:PRO30 4.0 0.0 1.0 O I:PRO30 4.0 0.0 1.0 N I:PRO30 4.1 0.0 1.0 CA I:CYS8 4.1 0.0 1.0 CB I:TYR31 4.1 0.0 1.0 N I:TYR31 4.2 0.0 1.0 CB I:CYS5 4.2 0.0 1.0 N I:CYS29 4.3 0.0 1.0 N I:CYS8 4.5 0.0 1.0 N I:CYS26 4.5 0.0 1.0 CA I:PRO30 4.5 0.0 1.0 O I:PRO6 4.5 0.0 1.0 OG I:SER7 4.6 0.0 1.0 C I:CYS8 4.7 0.0 1.0 N I:ASN9 4.8 0.0 1.0 CA I:TYR31 4.8 0.0 1.0 N I:ARG27 4.9 0.0 1.0 O I:ARG27 5.0 0.0 1.0

Zinc binding site 5 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2000 b:0.0 occ:1.00 SG J:CYS46 2.2 0.0 1.0 SG J:CYS10 2.4 0.0 1.0 SG J:CYS45 2.5 0.0 1.0 N J:CYS46 2.5 0.0 1.0 SG J:CYS7 2.7 0.0 1.0 OG J:SER9 2.7 0.0 1.0 CB J:CYS10 2.8 0.0 1.0 CA J:CYS46 2.9 0.0 1.0 CB J:CYS46 3.1 0.0 1.0 N J:CYS10 3.2 0.0 1.0 C J:CYS45 3.4 0.0 1.0 CA J:CYS10 3.6 0.0 1.0 CB J:CYS45 3.8 0.0 1.0 CB J:CYS7 3.9 0.0 1.0 O J:CYS45 4.1 0.0 1.0 CB J:SER9 4.1 0.0 1.0 CA J:CYS45 4.1 0.0 1.0 NE J:ARG43 4.2 0.0 1.0 C J:SER9 4.4 0.0 1.0 CB J:ARG43 4.4 0.0 1.0 C J:CYS46 4.4 0.0 1.0 N J:GLY11 4.5 0.0 1.0 C J:CYS10 4.6 0.0 1.0 N J:CYS45 4.6 0.0 1.0 CA J:SER9 4.7 0.0 1.0 O J:ARG43 4.8 0.0 1.0 N J:SER9 4.9 0.0 1.0 NH2 J:ARG43 4.9 0.0 1.0

Zinc binding site 6 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn2000 b:0.0 occ:1.00 SG L:CYS51 2.0 0.0 1.0 CB L:CYS51 2.4 0.0 1.0 SG L:CYS34 2.5 0.0 1.0 N L:CYS51 2.6 0.0 1.0 CB L:CYS34 2.6 0.0 1.0 SG L:CYS31 2.7 0.0 1.0 CA L:CYS51 2.9 0.0 1.0 SG L:CYS48 2.9 0.0 1.0 C L:ASP50 3.5 0.0 1.0 CB L:CYS48 3.6 0.0 1.0 C L:CYS51 3.7 0.0 1.0 O L:CYS51 3.7 0.0 1.0 CB L:ASP50 3.7 0.0 1.0 CB L:CYS31 4.0 0.0 1.0 CA L:ASP50 4.0 0.0 1.0 CA L:CYS34 4.0 0.0 1.0 N L:ASP50 4.2 0.0 1.0 N L:CYS34 4.3 0.0 1.0 O L:ASP50 4.5 0.0 1.0 C L:LYS49 4.8 0.0 1.0 N L:LYS49 4.8 0.0 1.0 N L:GLY52 4.9 0.0 1.0 C L:CYS34 4.9 0.0 1.0 CA L:CYS48 4.9 0.0 1.0

Zinc binding site 7 out of 7 in the Yeast Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Rna Polymerase III Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn1001 b:0.0 occ:1.00 CB R:CYS4 1.9 0.0 1.0 SG R:CYS25 2.2 0.0 1.0 SG R:CYS4 2.3 0.0 1.0 SG R:CYS7 2.3 0.0 1.0 SG R:CYS28 2.9 0.0 1.0 CA R:CYS4 3.3 0.0 1.0 CB R:CYS28 3.3 0.0 1.0 CB R:CYS25 3.9 0.0 1.0 N R:CYS4 4.0 0.0 1.0 CB R:CYS7 4.0 0.0 1.0 N R:GLY9 4.1 0.0 1.0 N R:HIS8 4.2 0.0 1.0 C R:CYS4 4.3 0.0 1.0 N R:CYS28 4.4 0.0 1.0 CE1 R:PHE12 4.4 0.0 1.0 N R:CYS7 4.4 0.0 1.0 CA R:CYS28 4.5 0.0 1.0 O R:VAL30 4.5 0.0 1.0 CA R:CYS7 4.6 0.0 1.0 C R:CYS7 4.7 0.0 1.0 CA R:GLY9 4.7 0.0 1.0 N R:LYS5 4.8 0.0 1.0 O R:GLY9 4.9 0.0 1.0 CA R:HIS8 4.9 0.0 1.0 CB R:ALA27 4.9 0.0 1.0 CA R:CYS25 4.9 0.0 1.0 N R:CYS25 4.9 0.0 1.0

Y.Han, C.Yan, S.Fishbain, I.Ivanov, Y.He. Structural Visualization of Rna Polymerase III Transcription Machineries. Cell Discov V. 4 40 2018.
ISSN: ESSN 2056-5968
PubMed: 30083386
DOI: 10.1038/S41421-018-0044-Z