Zinc in PDB 5m64: Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain

All present enzymatic activity of Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain (pdb code 5m64). 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 with A49 Tandem Winged Helix Domain, PDB code: 5m64:
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 with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:64.7 occ:1.00 SG A:CYS236 2.3 61.2 1.0 SG A:CYS105 2.3 64.0 1.0 SG A:CYS102 2.4 64.2 1.0 SG A:CYS233 2.4 63.6 1.0 CB A:CYS102 2.7 64.1 1.0 CB A:CYS233 3.3 64.3 1.0 CB A:CYS105 3.9 64.0 1.0 CB A:CYS236 4.0 61.3 1.0 CG A:ARG109 4.1 54.6 1.0 CA A:CYS102 4.1 63.0 1.0 O A:CYS236 4.2 62.1 1.0 N A:CYS236 4.3 61.0 1.0 CA A:ARG109 4.4 54.2 1.0 CA A:CYS236 4.6 61.3 1.0 O A:HIS107 4.7 61.1 1.0 CB A:ARG109 4.7 54.7 1.0 CA A:CYS233 4.8 64.5 1.0 O A:PHE108 4.9 52.0 1.0 N A:CYS105 4.9 65.3 1.0 N A:CYS102 4.9 61.4 1.0 C A:CYS236 4.9 61.7 1.0 N A:ARG109 4.9 53.8 1.0 CB A:ASN235 4.9 59.7 1.0 CD A:ARG109 4.9 54.7 1.0 CA A:CYS105 5.0 64.7 1.0

Zinc binding site 2 out of 6 in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:57.8 occ:1.00 NE2 A:HIS75 2.0 46.6 1.0 CD2 A:HIS75 2.2 53.4 1.0 SG A:CYS65 2.3 56.9 1.0 SG A:CYS72 2.3 52.2 1.0 SG A:CYS62 2.3 58.3 1.0 CB A:CYS65 2.9 56.3 1.0 CE1 A:HIS75 3.3 47.3 1.0 CG A:HIS75 3.6 53.8 1.0 OG1 A:THR64 3.6 56.9 1.0 CB A:CYS62 3.6 58.6 1.0 N A:CYS65 3.6 56.3 1.0 CA A:GLY55 3.8 52.1 1.0 CA A:CYS65 3.9 56.4 1.0 CB A:CYS72 4.0 52.5 1.0 ND1 A:HIS75 4.0 54.5 1.0 N A:GLY55 4.1 52.0 1.0 O A:ALA53 4.4 51.2 1.0 C A:GLY74 4.6 48.2 1.0 C A:GLY55 4.7 52.5 1.0 CA A:GLY74 4.7 48.6 1.0 O A:GLY74 4.7 48.3 1.0 CB A:HIS75 4.8 53.0 1.0 N A:GLY74 4.8 49.0 1.0 C A:LEU54 4.8 51.3 1.0 N A:ALA56 4.8 52.7 1.0 C A:THR64 4.8 58.0 1.0 CB A:THR64 4.9 57.9 1.0 N A:HIS75 4.9 48.1 1.0 C A:CYS65 4.9 57.0 1.0 CA A:CYS62 5.0 57.9 1.0

Zinc binding site 3 out of 6 in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:58.5 occ:1.00 SG B:CYS1107 2.3 62.0 1.0 SG B:CYS1131 2.3 60.1 1.0 SG B:CYS1104 2.3 55.8 1.0 SG B:CYS1128 2.3 53.1 1.0 CB B:CYS1107 2.8 61.9 1.0 CB B:CYS1104 2.9 56.3 1.0 CB B:CYS1128 3.0 53.5 1.0 CB B:CYS1131 3.6 60.6 1.0 CA B:CYS1107 4.0 60.8 1.0 N B:CYS1107 4.1 59.5 1.0 N B:CYS1131 4.3 60.0 1.0 CA B:CYS1104 4.4 56.9 1.0 OE2 B:GLU1106 4.4 58.9 1.0 CA B:CYS1128 4.5 53.4 1.0 CA B:CYS1131 4.6 59.4 1.0 C B:GLU1106 4.7 58.9 1.0 CD B:GLU1106 4.8 59.7 1.0 CG B:GLU1106 4.8 59.7 1.0 CA B:GLY1170 4.8 57.4 1.0 C B:CYS1104 4.9 57.9 1.0

Zinc binding site 4 out of 6 in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:82.6 occ:1.00 SG I:CYS13 2.3 79.3 1.0 SG I:CYS30 2.3 76.5 1.0 CB I:CYS30 2.3 76.8 1.0 NH2 M:ARG59 2.8 72.2 1.0 CA I:CYS30 3.5 78.5 1.0 OD1 I:ASP15 3.7 73.3 1.0 SG I:CYS10 3.8 65.0 1.0 CZ M:ARG59 3.9 64.5 1.0 CB I:CYS13 4.0 77.8 1.0 CB I:CYS10 4.2 65.4 1.0 NH1 M:ARG59 4.3 72.6 1.0 N I:CYS30 4.3 79.7 1.0 O I:CYS33 4.5 72.0 1.0 CG I:ASP15 4.6 71.1 1.0 OD2 I:ASP15 4.6 73.8 1.0 C I:CYS30 4.7 79.4 1.0 N I:SER31 4.8 75.8 1.0 NE2 I:GLN32 4.8 78.8 1.0

Zinc binding site 5 out of 6 in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:53.9 occ:1.00 SG J:CYS10 2.3 54.3 1.0 SG J:CYS45 2.3 52.0 1.0 SG J:CYS7 2.4 56.2 1.0 SG J:CYS46 2.4 53.9 1.0 CB J:CYS10 2.6 53.6 1.0 N J:CYS46 2.8 52.3 1.0 CA J:CYS46 3.1 53.0 1.0 C J:CYS45 3.1 53.1 1.0 CB J:CYS7 3.1 56.7 1.0 CB J:CYS46 3.3 53.7 1.0 CB J:CYS45 3.3 52.2 1.0 O J:CYS45 3.5 53.7 1.0 N J:CYS10 3.7 52.1 1.0 CA J:CYS10 3.7 52.6 1.0 CA J:CYS45 3.8 52.8 1.0 OG J:SER9 4.2 51.2 1.0 C J:CYS46 4.5 53.3 1.0 CA J:CYS7 4.6 56.0 1.0 CB J:MET49 4.6 52.3 1.0 N J:CYS45 4.6 52.8 1.0 N J:GLY11 4.6 54.3 1.0 C J:CYS10 4.7 52.7 1.0 C J:SER9 4.9 52.8 1.0 C J:CYS7 5.0 55.8 1.0

Zinc binding site 6 out of 6 in the Rna Polymerase I Elongation Complex with A49 Tandem Winged Helix Domain


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 with A49 Tandem Winged Helix Domain within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:68.1 occ:1.00 SG L:CYS51 2.3 67.2 1.0 SG L:CYS34 2.3 64.1 1.0 SG L:CYS31 2.3 59.4 1.0 SG L:CYS48 2.3 71.3 1.0 CB L:CYS48 3.0 71.1 1.0 OD1 L:ASP50 3.0 70.5 1.0 CB L:CYS34 3.3 64.5 1.0 CB L:CYS31 3.5 60.0 1.0 N L:CYS34 3.8 66.1 1.0 CB L:CYS51 3.9 68.0 1.0 CG L:ASP50 4.0 70.1 1.0 CA L:CYS34 4.2 65.6 1.0 N L:CYS51 4.2 69.5 1.0 OD2 L:ASP50 4.3 71.2 1.0 CA L:CYS48 4.4 71.4 1.0 CA L:CYS51 4.6 68.9 1.0 CB L:HIS53 4.6 64.3 1.0 O L:CYS51 4.6 69.5 1.0 OG L:SER36 4.7 60.9 1.0 N L:GLU33 4.8 64.0 1.0 C L:GLU33 4.9 64.8 1.0 C L:CYS51 4.9 69.1 1.0 CA L:CYS31 4.9 59.8 1.0 C L:CYS48 5.0 70.7 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