Zinc in PDB 5oa1: Rna Polymerase I Pre-Initiation Complex

All present enzymatic activity of Rna Polymerase I Pre-Initiation Complex:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Pre-Initiation Complex (pdb code 5oa1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Rna Polymerase I Pre-Initiation Complex, PDB code: 5oa1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:0.1 occ:1.00 SG A:CYS105 2.2 0.3 1.0 SG A:CYS233 2.4 0.2 1.0 SG A:CYS102 2.4 0.9 1.0 SG A:CYS236 2.4 0.8 1.0 CB A:CYS102 3.1 0.1 1.0 CB A:CYS233 3.3 0.3 1.0 CB A:CYS105 3.3 0.3 1.0 O A:CYS236 3.6 0.3 1.0 N A:CYS236 3.7 0.9 1.0 CB A:CYS236 3.7 0.9 1.0 N A:CYS105 3.8 1.0 1.0 CA A:CYS236 4.1 0.4 1.0 CA A:CYS105 4.1 0.9 1.0 C A:CYS236 4.3 0.8 1.0 CB A:ASN235 4.5 0.9 1.0 CA A:CYS102 4.6 0.4 1.0 CA A:CYS233 4.8 0.2 1.0 C A:ASN235 4.8 0.3 1.0 C A:CYS105 4.9 0.3 1.0 N A:HIS106 4.9 0.6 1.0 CB A:PHE104 5.0 0.1 1.0

Zinc binding site 2 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:95.4 occ:1.00 NE2 A:HIS75 2.0 92.3 1.0 SG A:CYS65 2.2 92.3 1.0 SG A:CYS62 2.3 94.9 1.0 SG A:CYS72 2.3 92.9 1.0 CD2 A:HIS75 2.7 92.3 1.0 CB A:CYS62 3.0 90.8 1.0 CE1 A:HIS75 3.1 92.0 1.0 CB A:CYS65 3.3 89.3 1.0 CB A:CYS72 3.7 89.0 1.0 N A:CYS65 3.7 90.1 1.0 CG A:HIS75 4.0 90.5 1.0 CA A:CYS65 4.0 89.9 1.0 ND1 A:HIS75 4.1 92.2 1.0 CA A:GLY55 4.3 81.8 1.0 CD A:PRO73 4.4 90.2 1.0 CA A:CYS72 4.4 88.5 1.0 CA A:CYS62 4.5 91.1 1.0 N A:GLY66 4.6 89.8 1.0 C A:CYS65 4.6 93.2 1.0 N A:GLY74 4.6 85.8 1.0 CB A:THR64 4.7 93.7 1.0 C A:THR64 4.8 94.5 1.0 N A:PRO73 4.9 87.8 1.0 N A:ALA56 4.9 83.7 1.0 C A:CYS72 4.9 91.5 1.0 CA A:GLY74 4.9 85.5 1.0 N A:LEU67 5.0 89.2 1.0

Zinc binding site 3 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:79.3 occ:1.00 SG B:CYS1131 2.2 88.5 1.0 SG B:CYS1104 2.2 81.6 1.0 SG B:CYS1128 2.3 84.6 1.0 SG B:CYS1107 2.4 88.7 1.0 CB B:CYS1104 3.2 76.8 1.0 CB B:CYS1107 3.3 85.5 1.0 CB B:CYS1131 3.3 86.2 1.0 CB B:CYS1128 3.4 81.5 1.0 N B:CYS1107 3.7 85.1 1.0 N B:CYS1131 3.8 86.3 1.0 CA B:CYS1107 4.1 84.9 1.0 CA B:CYS1131 4.2 87.1 1.0 CB B:ARG1130 4.3 83.0 1.0 OG1 B:THR1112 4.3 0.9 1.0 CB B:GLU1106 4.4 86.4 1.0 CG B:ARG1130 4.6 89.1 1.0 C B:GLU1106 4.6 88.1 1.0 CA B:CYS1104 4.6 76.2 1.0 C B:ARG1130 4.8 89.9 1.0 OG B:SER1109 4.8 0.5 1.0 CA B:CYS1128 4.8 82.0 1.0 CA B:GLU1106 4.9 83.9 1.0 CA B:ARG1130 4.9 84.5 1.0 C B:CYS1107 4.9 89.3 1.0

Zinc binding site 4 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.0 occ:1.00 SG I:CYS30 2.2 0.7 1.0 SG I:CYS13 2.5 0.4 1.0 CB I:CYS30 2.8 0.9 1.0 SG I:CYS10 3.0 0.9 1.0 SG I:CYS33 3.1 0.3 1.0 CB I:CYS10 3.5 0.8 1.0 O I:CYS33 3.8 0.5 1.0 CB I:CYS13 4.1 0.7 1.0 N I:CYS33 4.2 0.5 1.0 CA I:CYS30 4.3 0.2 1.0 CB I:ALA35 4.5 0.3 1.0 CB I:CYS33 4.6 0.7 1.0 CB I:GLN32 4.6 0.2 1.0 CB I:ASP15 4.6 0.5 1.0 N I:CYS13 4.6 0.5 1.0 C I:CYS33 4.7 0.2 1.0 CA I:CYS33 4.7 0.4 1.0 C I:CYS30 4.9 0.7 1.0 CA I:CYS13 5.0 0.3 1.0 CA I:CYS10 5.0 0.1 1.0

Zinc binding site 5 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:0.2 occ:1.00 SG I:CYS86 3.1 0.9 1.0 SG I:CYS89 3.1 0.6 1.0 SG I:CYS114 3.2 0.7 1.0 CB I:GLN88 3.7 0.9 1.0 CB I:SER116 4.1 0.7 1.0 CB I:CYS86 4.2 0.6 1.0 N I:CYS89 4.2 0.9 1.0 CG I:GLN88 4.3 0.3 1.0 SG I:CYS117 4.3 0.1 1.0 CB I:ASN91 4.4 0.3 1.0 CB I:CYS89 4.5 0.9 1.0 OG I:SER116 4.6 0.7 1.0 CB I:CYS114 4.6 1.0 1.0 CA I:GLN88 4.8 0.1 1.0 N I:GLY90 4.8 0.5 1.0 C I:GLN88 4.9 0.9 1.0 CA I:CYS89 4.9 0.7 1.0

Zinc binding site 6 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:0.1 occ:1.00 SG J:CYS7 2.2 1.0 1.0 SG J:CYS46 2.3 0.6 1.0 SG J:CYS45 2.3 0.2 1.0 SG J:CYS10 2.6 97.7 1.0 CB J:CYS7 3.1 99.2 1.0 N J:CYS46 3.3 97.3 1.0 CB J:CYS45 3.5 95.9 1.0 CB J:CYS46 3.6 98.9 1.0 CA J:CYS46 3.6 97.6 1.0 CB J:CYS10 3.7 92.5 1.0 C J:CYS45 3.7 0.5 1.0 N J:CYS10 3.7 90.8 1.0 CA J:CYS45 4.2 96.3 1.0 NE J:ARG43 4.2 84.9 1.0 O J:CYS45 4.2 99.9 1.0 CA J:CYS10 4.3 91.2 1.0 CB J:SER9 4.4 94.1 1.0 CA J:CYS7 4.5 98.1 1.0 N J:GLY11 4.7 93.0 1.0 C J:SER9 4.8 93.8 1.0 C J:CYS7 4.8 98.7 1.0 CB J:ARG43 4.8 95.6 1.0 O J:CYS7 4.9 98.0 1.0 CD J:ARG43 4.9 87.4 1.0 CB J:LYS12 4.9 1.0 1.0 NH2 J:ARG43 4.9 78.6 1.0 N J:SER9 4.9 91.3 1.0 CA J:SER9 4.9 90.3 1.0 N J:LYS12 5.0 97.4 1.0 N J:CYS45 5.0 97.5 1.0 C J:CYS10 5.0 95.7 1.0

Zinc binding site 7 out of 7 in the Rna Polymerase I Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase I Pre-Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.5 occ:1.00 SG L:CYS34 2.4 0.1 1.0 SG L:CYS51 2.4 0.6 1.0 SG L:CYS31 2.4 0.0 1.0 SG L:CYS48 2.4 0.2 1.0 CB L:CYS48 2.9 0.5 1.0 CB L:CYS31 3.3 0.4 1.0 CB L:CYS51 3.6 0.6 1.0 CB L:CYS34 3.7 0.9 1.0 O L:CYS51 3.7 0.9 1.0 N L:CYS51 3.7 0.4 1.0 OG L:SER36 4.0 0.6 1.0 CA L:CYS51 4.0 0.5 1.0 N L:CYS34 4.0 0.2 1.0 C L:CYS51 4.2 0.9 1.0 CA L:CYS48 4.4 0.2 1.0 CB L:HIS53 4.4 0.0 1.0 CA L:CYS34 4.4 0.7 1.0 CB L:ASP50 4.7 0.4 1.0 C L:ASP50 4.7 0.6 1.0 CA L:CYS31 4.7 0.5 1.0 C L:CYS48 4.9 0.1 1.0 N L:HIS53 5.0 0.2 1.0

Y.Sadian, L.Tafur, J.Kosinski, A.J.Jakobi, R.Wetzel, K.Buczak, W.J.Hagen, M.Beck, C.Sachse, C.W.Muller. Structural Insights Into Transcription Initiation By Yeast Rna Polymerase I. Embo J. V. 36 2698 2017.
ISSN: ESSN 1460-2075
PubMed: 28739580
DOI: 10.15252/EMBJ.201796958