Zinc in PDB 5m5y: Rna Polymerase I Elongation Complex 2

All present enzymatic activity of Rna Polymerase I Elongation Complex 2:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Elongation Complex 2 (pdb code 5m5y). 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 2, PDB code: 5m5y:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:76.9 occ:1.00 SG A:CYS236 2.3 77.3 1.0 SG A:CYS105 2.3 79.6 1.0 SG A:CYS233 2.4 71.2 1.0 SG A:CYS102 2.4 78.2 1.0 CB A:CYS102 2.8 78.9 1.0 CB A:CYS233 3.2 71.5 1.0 CB A:CYS105 3.7 80.9 1.0 N A:CYS105 4.1 85.0 1.0 CB A:CYS236 4.1 77.7 1.0 O A:CYS236 4.2 77.7 1.0 CA A:CYS102 4.3 77.5 1.0 N A:CYS236 4.3 76.6 1.0 CA A:CYS105 4.5 82.1 1.0 CA A:CYS236 4.7 76.8 1.0 CA A:CYS233 4.7 71.7 1.0 O A:HIS107 4.8 81.5 1.0 SD A:MET238 4.8 88.5 1.0 C A:CYS236 4.9 76.7 1.0 CB A:ASN235 5.0 72.0 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:59.6 occ:1.00 NE2 A:HIS75 2.0 46.1 1.0 SG A:CYS65 2.3 59.5 1.0 SG A:CYS72 2.4 55.9 1.0 SG A:CYS62 2.4 65.5 1.0 CD2 A:HIS75 2.7 49.9 1.0 CB A:CYS65 3.2 59.1 1.0 CE1 A:HIS75 3.2 46.4 1.0 CB A:CYS62 3.3 65.9 1.0 N A:CYS65 3.4 59.4 1.0 CB A:CYS72 3.9 56.3 1.0 CG A:HIS75 3.9 50.8 1.0 CA A:CYS65 3.9 59.1 1.0 ND1 A:HIS75 4.1 51.7 1.0 O A:ALA53 4.2 55.7 1.0 CB A:THR64 4.3 61.3 1.0 CA A:GLY55 4.3 57.4 1.0 C A:THR64 4.5 60.9 1.0 N A:THR64 4.6 61.6 1.0 N A:GLY55 4.7 57.7 1.0 CA A:THR64 4.7 60.9 1.0 CA A:CYS62 4.7 67.4 1.0 O A:LEU54 4.8 54.6 1.0 N A:GLY66 4.8 58.9 1.0 C A:CYS65 4.9 58.8 1.0 CA A:GLY74 4.9 47.8 1.0 C A:LEU54 4.9 54.6 1.0 N A:GLY74 4.9 48.7 1.0 C A:GLY74 5.0 47.2 1.0 CA A:CYS72 5.0 58.4 1.0 CG2 A:THR64 5.0 60.3 1.0 C A:GLY55 5.0 57.4 1.0 N A:ALA56 5.0 58.0 1.0

Zinc binding site 3 out of 6 in the Rna Polymerase I Elongation Complex 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:62.4 occ:1.00 SG B:CYS1107 2.3 62.0 1.0 SG B:CYS1128 2.4 60.9 1.0 SG B:CYS1104 2.4 59.2 1.0 SG B:CYS1131 2.4 67.9 1.0 CB B:CYS1107 2.7 62.7 1.0 N B:CYS1107 3.4 63.0 1.0 CB B:CYS1128 3.4 61.1 1.0 CB B:CYS1131 3.5 67.8 1.0 CG B:GLU1106 3.6 68.5 1.0 CA B:CYS1107 3.7 62.7 1.0 CB B:CYS1104 3.8 58.8 1.0 OE2 B:GLU1106 4.0 63.4 1.0 N B:CYS1131 4.0 65.4 1.0 CD B:GLU1106 4.1 67.3 1.0 C B:GLU1106 4.3 67.0 1.0 CA B:CYS1131 4.4 65.7 1.0 CB B:GLU1106 4.7 68.2 1.0 C B:CYS1107 4.7 62.5 1.0 CB B:ARG1130 4.7 67.0 1.0 CA B:GLY1170 4.7 67.2 1.0 N B:GLU1106 4.8 62.7 1.0 CA B:CYS1128 4.8 62.2 1.0 CA B:GLU1106 4.8 64.6 1.0 C B:ARG1130 5.0 66.2 1.0

Zinc binding site 4 out of 6 in the Rna Polymerase I Elongation Complex 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.9 occ:1.00 SG I:CYS13 2.3 0.1 1.0 SG I:CYS30 2.3 0.9 1.0 CB I:CYS30 2.4 0.3 1.0 SG I:CYS10 3.0 99.2 1.0 O I:CYS33 3.7 0.4 1.0 NE2 I:GLN32 3.8 0.6 1.0 SG I:CYS33 3.8 0.6 1.0 CA I:CYS30 3.9 0.1 1.0 CB I:CYS13 4.0 0.3 1.0 CB I:CYS10 4.0 0.7 1.0 NH1 M:ARG59 4.1 0.6 1.0 CB I:ALA35 4.4 0.7 1.0 CD I:GLN32 4.4 94.4 1.0 CE2 I:TYR37 4.5 0.1 1.0 N I:CYS30 4.6 0.7 1.0 N I:CYS13 4.7 0.0 1.0 C I:CYS30 4.7 0.8 1.0 C I:CYS33 4.8 0.2 1.0 CA I:CYS13 4.9 0.4 1.0 CG I:GLN32 5.0 93.2 1.0

Zinc binding site 5 out of 6 in the Rna Polymerase I Elongation Complex 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:45.1 occ:1.00 SG J:CYS10 2.3 45.1 1.0 SG J:CYS45 2.4 45.5 1.0 SG J:CYS46 2.4 43.5 1.0 SG J:CYS7 2.4 47.7 1.0 N J:CYS46 2.6 43.5 1.0 C J:CYS45 2.8 43.9 1.0 CA J:CYS46 2.9 43.5 1.0 O J:CYS45 3.0 43.2 1.0 CB J:CYS10 3.1 44.4 1.0 CB J:CYS46 3.2 43.1 1.0 CB J:CYS45 3.3 44.2 1.0 CB J:CYS7 3.5 47.0 1.0 N J:CYS10 3.6 41.9 1.0 CA J:CYS45 3.6 44.2 1.0 CA J:CYS10 4.0 43.2 1.0 C J:CYS46 4.4 44.5 1.0 N J:CYS45 4.6 44.2 1.0 CB J:SER9 4.6 41.2 1.0 N J:GLY11 4.7 45.9 1.0 C J:SER9 4.7 41.7 1.0 CA J:CYS7 4.9 47.0 1.0 C J:CYS10 4.9 44.1 1.0 N J:SER9 4.9 42.6 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:83.6 occ:1.00 SG L:CYS31 2.3 66.1 1.0 SG L:CYS48 2.3 98.7 1.0 SG L:CYS51 2.3 76.8 1.0 SG L:CYS34 2.3 68.8 1.0 OE2 L:GLU33 2.6 70.3 1.0 CB L:CYS48 2.8 0.4 1.0 CD L:GLU33 3.4 74.5 1.0 CB L:CYS34 3.6 69.0 1.0 CB L:CYS31 3.6 66.2 1.0 CG L:GLU33 3.8 73.8 1.0 CB L:CYS51 4.0 78.1 1.0 N L:CYS34 4.1 70.9 1.0 N L:CYS51 4.2 81.6 1.0 CA L:CYS48 4.3 0.5 1.0 OE1 L:GLU33 4.3 70.6 1.0 OG L:SER36 4.4 67.8 1.0 O L:CYS51 4.4 79.7 1.0 CA L:CYS34 4.5 71.3 1.0 CA L:CYS51 4.6 79.1 1.0 C L:CYS51 4.8 78.7 1.0 N L:GLU33 4.9 68.4 1.0 CA L:CYS31 5.0 67.6 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