Zinc in PDB 5m5w: Rna Polymerase I Open Complex

All present enzymatic activity of Rna Polymerase I Open Complex:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Open Complex (pdb code 5m5w). 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 Open Complex, PDB code: 5m5w:
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 Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:88.1 occ:1.00 SG A:CYS236 2.3 0.8 1.0 SG A:CYS105 2.3 91.3 1.0 SG A:CYS233 2.3 92.2 1.0 SG A:CYS102 2.3 89.0 1.0 CB A:CYS102 3.0 83.1 1.0 CB A:CYS233 3.3 88.3 1.0 CB A:CYS105 3.7 89.3 1.0 CE A:MET238 4.0 0.8 1.0 CB A:CYS236 4.0 0.9 1.0 OD1 A:ASN235 4.2 0.2 1.0 N A:CYS105 4.3 89.0 1.0 CA A:CYS102 4.5 81.4 1.0 O A:PHE108 4.6 86.2 1.0 CA A:CYS105 4.6 88.9 1.0 CG A:MET238 4.7 0.1 1.0 CA A:CYS233 4.7 88.2 1.0 OG A:SER240 4.9 93.4 1.0 O A:CYS236 5.0 0.3 1.0

Zinc binding site 2 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:75.4 occ:1.00 NE2 A:HIS75 2.0 72.3 1.0 SG A:CYS65 2.3 72.3 1.0 SG A:CYS72 2.3 72.9 1.0 SG A:CYS62 2.3 74.9 1.0 CD2 A:HIS75 2.5 72.3 1.0 CB A:CYS65 3.2 69.3 1.0 CB A:CYS62 3.2 70.8 1.0 CE1 A:HIS75 3.3 72.0 1.0 N A:CYS65 3.3 70.1 1.0 CG A:HIS75 3.8 70.5 1.0 CA A:CYS65 3.8 69.9 1.0 CB A:CYS72 3.9 69.0 1.0 CB A:THR64 4.0 73.7 1.0 ND1 A:HIS75 4.1 72.2 1.0 C A:THR64 4.3 74.5 1.0 CA A:GLY55 4.3 61.8 1.0 O A:ALA53 4.4 67.5 1.0 CA A:THR64 4.5 70.7 1.0 N A:THR64 4.5 71.3 1.0 N A:GLY55 4.6 62.4 1.0 CG2 A:THR64 4.6 72.0 1.0 CA A:CYS62 4.7 71.1 1.0 C A:CYS65 4.8 73.2 1.0 N A:GLY66 4.8 69.8 1.0 OG1 A:THR64 4.9 71.6 1.0 C A:LEU54 5.0 65.4 1.0

Zinc binding site 3 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:59.3 occ:1.00 SG B:CYS1131 2.3 68.5 1.0 SG B:CYS1107 2.3 68.7 1.0 SG B:CYS1128 2.3 64.6 1.0 SG B:CYS1104 2.3 61.6 1.0 CB B:CYS1107 2.9 65.5 1.0 CB B:CYS1131 3.2 66.2 1.0 CB B:CYS1104 3.3 56.8 1.0 CB B:CYS1128 3.4 61.5 1.0 OE2 B:GLU1106 3.6 0.8 1.0 N B:CYS1107 3.9 65.1 1.0 CA B:CYS1107 4.1 64.9 1.0 CD B:GLU1106 4.1 0.2 1.0 N B:CYS1131 4.1 66.3 1.0 CG B:GLU1106 4.2 80.0 1.0 CA B:CYS1131 4.2 67.1 1.0 CA B:CYS1104 4.7 56.2 1.0 CA B:CYS1128 4.8 62.0 1.0 C B:GLU1106 4.8 68.1 1.0 OE1 B:GLU1106 4.9 98.4 1.0 CG2 B:THR1112 4.9 81.8 1.0

Zinc binding site 4 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.0 occ:1.00 SG I:CYS13 2.3 0.4 1.0 SG I:CYS30 2.3 0.7 1.0 OD1 I:ASP15 2.8 0.9 1.0 CB I:CYS30 2.9 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 3.6 0.8 1.0 CG I:ASP15 3.8 0.8 1.0 NH2 M:ARG59 3.9 0.0 1.0 CB I:CYS13 4.0 0.7 1.0 OD2 I:ASP15 4.1 0.8 1.0 CA I:CYS30 4.4 0.2 1.0 CB I:ALA35 4.5 0.3 1.0 OD1 I:ASP12 4.5 0.4 1.0 CB I:CYS33 4.7 0.7 1.0 N I:CYS33 4.8 0.5 1.0

Zinc binding site 5 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:30.0 occ:1.00 SG I:CYS89 2.5 0.6 1.0 CB I:CYS117 2.6 0.4 1.0 NE2 I:GLN88 2.6 0.4 1.0 SG I:CYS114 3.2 0.7 1.0 CD I:GLN88 3.5 0.9 1.0 N I:CYS117 3.6 0.6 1.0 CA I:CYS117 3.7 0.1 1.0 CG I:GLN88 3.7 0.3 1.0 SG I:CYS117 3.8 0.1 1.0 CB I:CYS89 4.0 0.9 1.0 OD1 I:ASN91 4.2 0.1 1.0 SG I:CYS86 4.3 0.9 1.0 C I:SER116 4.3 0.6 1.0 CB I:CYS114 4.4 1.0 1.0 CB I:SER116 4.6 0.7 1.0 OE1 I:GLN88 4.6 0.6 1.0 N I:CYS89 4.7 0.9 1.0 CB I:CYS86 4.7 0.6 1.0 C I:CYS117 4.8 0.4 1.0 CA I:SER116 4.9 0.6 1.0 OG I:SER116 4.9 0.7 1.0 O I:SER116 4.9 0.8 1.0 CA I:CYS89 5.0 0.7 1.0

Zinc binding site 6 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:84.2 occ:1.00 N J:CYS46 2.3 77.3 1.0 SG J:CYS10 2.3 77.7 1.0 SG J:CYS46 2.3 81.6 1.0 SG J:CYS45 2.3 81.2 1.0 SG J:CYS7 2.3 82.0 1.0 C J:CYS45 2.5 80.5 1.0 CA J:CYS46 2.7 77.6 1.0 O J:CYS45 3.0 79.9 1.0 CB J:CYS45 3.0 75.9 1.0 CB J:CYS46 3.0 78.9 1.0 CB J:CYS10 3.1 72.5 1.0 CA J:CYS45 3.3 76.3 1.0 CB J:CYS7 3.4 79.2 1.0 N J:CYS10 3.4 70.8 1.0 CA J:CYS10 3.9 71.2 1.0 C J:CYS46 4.2 82.9 1.0 N J:CYS45 4.3 77.5 1.0 CB J:SER9 4.4 74.1 1.0 C J:SER9 4.5 73.8 1.0 N J:GLY11 4.6 73.0 1.0 CA J:CYS7 4.7 78.1 1.0 N J:SER9 4.7 71.3 1.0 CA J:SER9 4.8 70.3 1.0 C J:CYS7 4.8 78.7 1.0 C J:CYS10 4.8 75.7 1.0 N J:ARG47 4.8 80.5 1.0 NH2 J:ARG48 4.9 0.3 1.0 O J:CYS46 4.9 82.6 1.0 O J:CYS7 5.0 78.0 1.0

Zinc binding site 7 out of 7 in the Rna Polymerase I Open 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 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.5 occ:1.00 SG L:CYS48 2.3 0.2 1.0 SG L:CYS34 2.3 0.1 1.0 SG L:CYS31 2.3 0.0 1.0 SG L:CYS51 2.3 0.6 1.0 CB L:CYS48 2.7 0.5 1.0 CB L:CYS31 2.9 0.4 1.0 CB L:CYS34 3.7 0.9 1.0 CB L:CYS51 4.0 0.6 1.0 OG L:SER36 4.1 0.6 1.0 CA L:CYS48 4.2 0.2 1.0 N L:CYS51 4.2 0.4 1.0 CA L:CYS31 4.3 99.5 1.0 N L:CYS34 4.5 0.2 1.0 CA L:CYS51 4.6 0.5 1.0 CA L:CYS34 4.7 0.7 1.0 O L:CYS51 4.7 0.9 1.0 C L:CYS48 4.8 0.1 1.0 CD2 L:HIS53 4.8 0.9 1.0 N L:CYS48 4.9 0.5 1.0 CD2 L:LEU38 4.9 0.7 1.0 CB L:HIS53 4.9 0.0 1.0 C L:CYS51 4.9 0.9 1.0

L.Tafur, Y.Sadian, N.A.Hoffmann, A.J.Jakobi, R.Wetzel, W.J.Hagen, C.Sachse, C.W.Muller. Molecular Structures of Transcribing Rna Polymerase I. Mol. Cell V. 64 1135 2016.
ISSN: ISSN 1097-4164
PubMed: 27867008
DOI: 10.1016/J.MOLCEL.2016.11.013