Zinc in PDB 9g1x: Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit:
2.7.7.6;

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit (pdb code 9g1x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit, PDB code: 9g1x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:234.0 occ:1.00 NE2 A:HIS75 2.0 138.5 1.0 SG A:CYS72 2.3 181.9 1.0 SG A:CYS62 2.3 177.4 1.0 SG A:CYS65 2.3 191.3 1.0 CD2 A:HIS75 2.6 138.9 1.0 CB A:CYS62 2.8 168.8 1.0 CE1 A:HIS75 3.3 140.8 1.0 CB A:CYS65 3.3 171.1 1.0 CB A:CYS72 3.3 174.5 1.0 N A:CYS65 3.8 170.7 1.0 CG A:HIS75 3.9 135.5 1.0 CA A:CYS65 4.1 170.8 1.0 CA A:GLY55 4.2 157.9 1.0 ND1 A:HIS75 4.2 140.1 1.0 CA A:CYS72 4.2 171.5 1.0 CA A:CYS62 4.3 165.7 1.0 N A:ALA56 4.3 160.4 1.0 CB A:THR64 4.5 154.0 1.0 N A:GLY55 4.6 158.5 1.0 N A:GLY74 4.7 147.2 1.0 C A:GLY55 4.7 156.1 1.0 C A:CYS62 4.7 167.0 1.0 C A:CYS72 4.7 170.6 1.0 C A:THR64 4.7 154.2 1.0 CD A:PRO73 4.8 153.0 1.0 N A:GLY66 4.9 174.3 1.0 N A:THR64 4.9 161.3 1.0 O A:CYS62 4.9 169.9 1.0 CA A:GLY74 5.0 149.6 1.0 CA A:THR64 5.0 154.7 1.0 C A:CYS65 5.0 171.3 1.0

Zinc binding site 2 out of 5 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:300.6 occ:1.00 SG A:CYS105 2.3 216.4 1.0 SG A:CYS233 2.3 199.9 1.0 SG A:CYS102 2.3 203.5 1.0 SG A:CYS236 2.3 211.9 1.0 CB A:CYS105 2.6 204.6 1.0 CB A:CYS102 2.7 195.8 1.0 CB A:CYS233 3.2 192.6 1.0 O A:CYS236 3.5 211.2 1.0 N A:CYS105 3.6 204.6 1.0 CA A:CYS105 3.7 204.1 1.0 N A:CYS236 3.7 206.4 1.0 CB A:CYS236 3.8 206.2 1.0 CA A:CYS236 4.1 206.4 1.0 CA A:CYS102 4.2 193.3 1.0 C A:CYS236 4.2 208.6 1.0 CB A:ASN235 4.5 205.4 1.0 C A:ASN235 4.5 202.4 1.0 C A:CYS105 4.6 203.1 1.0 CA A:CYS233 4.7 191.1 1.0 N A:ASN235 4.7 205.1 1.0 C A:CYS102 4.7 192.1 1.0 O A:CYS102 4.8 191.6 1.0 CA A:ASN235 4.8 204.3 1.0 C A:PHE104 4.8 178.4 1.0 N A:HIS106 4.9 192.7 1.0 N A:CYS102 5.0 192.1 1.0

Zinc binding site 3 out of 5 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1701 b:261.5 occ:1.00 SG B:CYS1104 2.3 188.4 1.0 SG B:CYS1107 2.3 156.9 1.0 SG B:CYS1128 2.3 164.7 1.0 SG B:CYS1131 2.3 167.2 1.0 CB B:CYS1104 2.8 171.6 1.0 CB B:CYS1128 2.9 162.3 1.0 CB B:CYS1107 3.5 145.3 1.0 CB B:CYS1131 3.7 165.9 1.0 N B:CYS1131 4.0 159.9 1.0 CA B:CYS1104 4.3 160.3 1.0 N B:CYS1107 4.3 142.9 1.0 CA B:CYS1128 4.4 156.1 1.0 CA B:CYS1131 4.4 162.5 1.0 CG B:GLU1106 4.5 158.9 1.0 CA B:CYS1107 4.5 144.9 1.0 O B:GLY1170 4.7 171.7 1.0 OE2 B:GLU1106 4.8 166.1 1.0 N B:ARG1130 4.8 145.5 1.0 C B:CYS1104 4.8 161.7 1.0 CB B:ARG1130 4.9 145.3 1.0 N B:ARG1129 4.9 149.8 1.0 OG B:SER1109 4.9 159.5 1.0 C B:CYS1128 5.0 157.4 1.0

Zinc binding site 4 out of 5 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1701 b:239.6 occ:1.00 SG J:CYS10 2.3 156.5 1.0 SG J:CYS45 2.3 145.8 1.0 SG J:CYS46 2.3 156.2 1.0 SG J:CYS7 2.3 148.6 1.0 N J:CYS46 3.0 135.5 1.0 CB J:CYS7 3.2 136.9 1.0 CB J:CYS10 3.3 139.2 1.0 CA J:CYS46 3.3 130.6 1.0 CB J:CYS46 3.4 137.5 1.0 C J:CYS45 3.5 137.2 1.0 CB J:CYS45 3.6 138.3 1.0 N J:CYS10 3.8 134.2 1.0 O J:CYS45 4.0 140.5 1.0 CA J:CYS10 4.1 138.7 1.0 CA J:CYS45 4.2 134.9 1.0 N J:GLY11 4.5 133.4 1.0 NE J:ARG43 4.6 123.8 1.0 CA J:CYS7 4.6 132.1 1.0 NH2 J:ARG43 4.7 126.5 1.0 CB J:LYS12 4.7 133.6 1.0 C J:CYS46 4.8 127.6 1.0 N J:LYS12 4.8 146.1 1.0 C J:CYS10 4.9 138.0 1.0 CB J:SER9 4.9 132.5 1.0 C J:CYS7 4.9 140.2 1.0 C J:SER9 5.0 128.6 1.0 N J:CYS45 5.0 136.2 1.0

Zinc binding site 5 out of 5 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 11-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn1701 b:247.7 occ:1.00 SG L:CYS34 2.3 174.9 1.0 SG L:CYS51 2.3 170.4 1.0 SG L:CYS48 2.3 161.1 1.0 SG L:CYS31 2.3 152.2 1.0 CB L:CYS31 2.9 142.8 1.0 CB L:CYS48 3.1 150.4 1.0 CB L:CYS34 3.5 163.8 1.0 CB L:CYS51 3.8 156.2 1.0 N L:CYS34 3.8 162.2 1.0 CA L:CYS34 4.2 160.3 1.0 N L:CYS51 4.3 154.7 1.0 CA L:CYS31 4.4 134.2 1.0 CB L:HIS53 4.5 151.1 1.0 CA L:CYS51 4.5 151.8 1.0 CA L:CYS48 4.6 147.8 1.0 CB L:GLU33 4.7 163.4 1.0 O L:CYS51 4.7 152.1 1.0 C L:CYS34 4.8 157.5 1.0 C L:CYS51 4.8 153.0 1.0 N L:SER35 4.9 146.2 1.0 C L:GLU33 4.9 160.5 1.0 N L:GLU33 5.0 158.8 1.0

A.Santos-Aledo, A.Plaza-Pegueroles, M.Sanz-Murillo, F.M.Ruiz, P.Hou, J.Xu, D.Gil-Carton, D.Wang, C.Fernandez-Tornero. Cryo-Em Uncovers A Sequential Mechanism For Rna Polymerase I Pausing and Stalling at Abasic Dna Lesions. Nat Commun V. 16 5254 2025.
ISSN: ESSN 2041-1723
PubMed: 40480971
DOI: 10.1038/S41467-025-60536-4