Zinc in PDB 5m5x: Rna Polymerase I Elongation Complex 1

All present enzymatic activity of Rna Polymerase I Elongation Complex 1:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Elongation Complex 1 (pdb code 5m5x). 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 I Elongation Complex 1, PDB code: 5m5x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:54.1 occ:1.00 SG A:CYS236 2.3 55.4 1.0 SG A:CYS105 2.3 52.7 1.0 SG A:CYS102 2.3 54.1 1.0 SG A:CYS233 2.3 50.6 1.0 CB A:CYS102 2.7 54.8 1.0 CB A:CYS233 2.9 51.1 1.0 CB A:CYS105 3.7 52.7 1.0 CB A:CYS236 4.0 55.7 1.0 O A:CYS236 4.0 55.5 1.0 N A:CYS236 4.1 55.8 1.0 CA A:CYS102 4.2 55.2 1.0 N A:CYS105 4.4 54.1 1.0 CA A:CYS233 4.4 50.9 1.0 CA A:CYS236 4.5 55.6 1.0 SD A:MET238 4.5 57.7 1.0 C A:CYS236 4.7 55.3 1.0 CA A:CYS105 4.7 52.9 1.0 O A:PHE108 4.9 47.8 1.0 CB A:ASN235 4.9 54.4 1.0 N A:CYS102 5.0 54.9 1.0 O A:MET238 5.0 59.6 1.0 C A:CYS102 5.0 55.5 1.0

Zinc binding site 2 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:41.1 occ:1.00 NE2 A:HIS75 2.0 35.6 1.0 SG A:CYS65 2.3 39.8 1.0 SG A:CYS62 2.3 44.4 1.0 SG A:CYS72 2.3 42.3 1.0 CD2 A:HIS75 2.4 38.7 1.0 CB A:CYS62 3.0 44.5 1.0 CB A:CYS65 3.2 39.9 1.0 CE1 A:HIS75 3.3 35.4 1.0 N A:CYS65 3.5 39.8 1.0 CA A:GLY55 3.5 42.8 1.0 CG A:HIS75 3.7 38.4 1.0 N A:GLY55 3.9 42.1 1.0 CB A:CYS72 3.9 42.1 1.0 CA A:CYS65 3.9 39.6 1.0 ND1 A:HIS75 4.1 37.9 1.0 CB A:THR64 4.4 41.5 1.0 C A:GLY55 4.4 43.0 1.0 N A:ALA56 4.5 43.0 1.0 CA A:CYS62 4.5 45.5 1.0 C A:THR64 4.5 41.2 1.0 N A:THR64 4.6 41.5 1.0 N A:GLY66 4.7 40.2 1.0 CA A:THR64 4.7 41.0 1.0 C A:CYS65 4.9 39.3 1.0 C A:GLY74 4.9 36.3 1.0 CB A:HIS75 4.9 38.0 1.0 O A:ALA53 4.9 38.2 1.0 C A:LEU54 4.9 39.1 1.0 CA A:CYS72 4.9 42.2 1.0 O A:GLY74 5.0 36.3 1.0 CA A:GLY74 5.0 37.1 1.0

Zinc binding site 3 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:47.9 occ:1.00 SG B:CYS1107 2.3 50.0 1.0 SG B:CYS1128 2.3 43.2 1.0 SG B:CYS1104 2.3 51.5 1.0 SG B:CYS1131 2.3 47.9 1.0 CB B:CYS1107 2.8 49.2 1.0 OE2 B:GLU1106 3.2 49.2 1.0 CB B:CYS1128 3.3 43.3 1.0 CB B:CYS1131 3.5 47.9 1.0 CB B:CYS1104 3.6 50.7 1.0 N B:CYS1107 3.6 48.6 1.0 CD B:GLU1106 3.7 52.4 1.0 CA B:CYS1107 3.8 48.4 1.0 CG B:GLU1106 3.9 53.4 1.0 N B:CYS1131 4.0 46.1 1.0 CA B:CYS1131 4.4 47.0 1.0 OE1 B:GLU1106 4.4 49.3 1.0 CA B:CYS1128 4.6 45.0 1.0 C B:GLU1106 4.7 51.2 1.0 O B:CYS1128 4.7 46.8 1.0 CB B:ARG1130 4.8 42.6 1.0 C B:CYS1107 4.9 47.9 1.0 C B:CYS1128 4.9 46.0 1.0 CA B:CYS1104 5.0 50.6 1.0 N B:GLY1108 5.0 50.3 1.0

Zinc binding site 4 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:76.7 occ:1.00 CB I:CYS30 2.3 71.3 1.0 SG I:CYS13 2.3 68.9 1.0 SG I:CYS30 2.3 70.7 1.0 SG I:CYS10 3.3 68.8 1.0 CB I:CYS10 3.4 68.9 1.0 O I:CYS33 3.7 63.8 1.0 CA I:CYS30 3.8 73.8 1.0 CB I:CYS13 4.1 68.8 1.0 OD2 I:ASP15 4.1 70.6 1.0 SG I:CYS33 4.1 65.6 1.0 CB I:ASP15 4.2 70.3 1.0 NH1 M:ARG59 4.5 73.9 1.0 N I:CYS30 4.5 75.1 1.0 C I:CYS30 4.7 74.7 1.0 N I:CYS33 4.7 65.0 1.0 CB I:ALA35 4.7 68.5 1.0 CG I:ASP15 4.7 72.0 1.0 C I:CYS33 4.8 65.8 1.0 N I:SER31 4.8 68.8 1.0 CA I:CYS10 5.0 68.9 1.0

Zinc binding site 5 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:34.9 occ:1.00 CB J:CYS46 2.0 33.2 1.0 CA J:CYS46 2.3 33.6 1.0 SG J:CYS10 2.3 34.8 1.0 SG J:CYS7 2.4 37.0 1.0 N J:CYS46 2.4 33.0 1.0 SG J:CYS46 2.4 33.4 1.0 SG J:CYS45 2.5 33.3 1.0 C J:CYS45 2.9 32.5 1.0 CB J:CYS10 3.0 34.5 1.0 O J:CYS45 3.3 32.5 1.0 CB J:CYS7 3.3 36.6 1.0 CB J:CYS45 3.7 32.7 1.0 N J:CYS10 3.7 33.3 1.0 C J:CYS46 3.8 34.1 1.0 CA J:CYS45 3.9 32.4 1.0 CA J:CYS10 4.0 34.0 1.0 O J:CYS46 4.4 35.3 1.0 N J:ARG47 4.7 33.3 1.0 N J:CYS45 4.7 32.0 1.0 CA J:CYS7 4.7 37.0 1.0 N J:GLY11 4.7 35.1 1.0 C J:SER9 4.9 33.0 1.0 O J:ARG43 4.9 37.6 1.0 C J:CYS10 4.9 34.5 1.0 CB J:SER9 4.9 32.6 1.0 C J:CYS7 4.9 37.0 1.0

Zinc binding site 6 out of 6 in the Rna Polymerase I Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:49.1 occ:1.00 SG L:CYS48 2.3 52.5 1.0 SG L:CYS51 2.3 49.5 1.0 SG L:CYS31 2.3 41.6 1.0 CB L:CYS48 2.3 52.8 1.0 SG L:CYS34 2.3 42.5 1.0 CB L:CYS31 3.2 41.5 1.0 O L:CYS51 3.7 50.1 1.0 CB L:CYS34 3.8 42.9 1.0 CB L:CYS51 3.8 50.4 1.0 CA L:CYS48 3.8 53.6 1.0 N L:CYS51 3.9 51.6 1.0 CA L:CYS51 4.2 50.6 1.0 OG L:SER36 4.2 43.1 1.0 C L:CYS51 4.3 50.1 1.0 CA L:CYS31 4.4 42.1 1.0 N L:CYS34 4.4 43.4 1.0 C L:CYS48 4.5 53.6 1.0 N L:CYS48 4.5 54.3 1.0 CA L:CYS34 4.7 43.8 1.0 N L:ASP50 4.9 53.1 1.0 C L:ASP50 5.0 54.3 1.0 CB L:HIS53 5.0 56.2 1.0 O L:CYS48 5.0 53.4 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