Zinc in PDB 9g2c: Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State

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

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State (pdb code 9g2c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State, PDB code: 9g2c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State


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, Open State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3001 b:283.9 occ:1.00 SG B:CYS1104 2.3 197.2 1.0 SG B:CYS1131 2.3 205.3 1.0 SG B:CYS1107 2.3 216.6 1.0 SG B:CYS1128 2.3 216.9 1.0 CB B:CYS1131 2.9 197.9 1.0 N B:CYS1131 2.9 194.8 1.0 CB B:CYS1107 3.1 209.0 1.0 CA B:CYS1131 3.2 194.7 1.0 CB B:CYS1128 3.6 204.2 1.0 C B:ARG1130 3.7 175.2 1.0 N B:CYS1107 3.8 207.8 1.0 OE1 B:GLU1106 3.8 210.9 1.0 CB B:CYS1104 3.9 194.4 1.0 CA B:CYS1107 4.0 208.6 1.0 CB B:ARG1130 4.1 176.0 1.0 O B:ARG1130 4.4 174.4 1.0 CA B:ARG1130 4.4 176.7 1.0 O B:CYS1128 4.6 207.6 1.0 C B:CYS1131 4.7 190.6 1.0 N B:ARG1130 4.8 181.2 1.0 CG B:ARG1130 4.9 174.3 1.0 CA B:CYS1128 4.9 206.0 1.0 CB B:GLU1106 4.9 206.7 1.0 C B:CYS1128 4.9 208.5 1.0 C B:GLU1106 4.9 206.7 1.0 CA B:CYS1104 4.9 194.2 1.0 CD B:GLU1106 5.0 208.9 1.0

Zinc binding site 2 out of 4 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State


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, Open State within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3001 b:334.8 occ:1.00 OD1 I:ASP12 2.0 222.7 1.0 SG I:CYS33 2.3 248.8 1.0 SG I:CYS30 2.3 215.3 1.0 SG I:CYS13 2.3 214.8 1.0 SG I:CYS10 2.3 213.1 1.0 CB I:CYS33 2.9 238.6 1.0 CB I:CYS13 3.0 202.6 1.0 CG I:ASP12 3.2 218.3 1.0 CA I:CYS33 3.3 237.6 1.0 CB I:CYS10 3.4 202.0 1.0 N I:CYS13 3.6 202.8 1.0 CB I:CYS30 3.7 210.2 1.0 OD2 I:ASP12 3.9 220.7 1.0 CA I:CYS13 3.9 201.1 1.0 O I:CYS33 4.1 237.9 1.0 O I:CYS30 4.1 209.3 1.0 C I:CYS33 4.2 237.9 1.0 CB I:ASP12 4.4 214.2 1.0 N I:CYS33 4.4 237.6 1.0 C I:CYS13 4.7 200.9 1.0 C I:ASP12 4.7 210.4 1.0 CA I:CYS30 4.8 210.1 1.0 CA I:CYS10 4.9 198.8 1.0 O I:ASP15 4.9 167.2 1.0 CD1 I:LEU17 4.9 188.0 1.0 C I:CYS30 4.9 209.5 1.0 CA I:ASP12 5.0 210.3 1.0

Zinc binding site 3 out of 4 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State


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, Open State within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn3001 b:242.9 occ:1.00 CB J:CYS10 2.0 144.4 1.0 SG J:CYS46 2.3 173.2 1.0 SG J:CYS45 2.3 161.5 1.0 SG J:CYS10 2.3 162.3 1.0 SG J:CYS7 2.3 139.7 1.0 NE J:ARG43 3.0 141.6 1.0 CA J:CYS10 3.2 134.8 1.0 N J:CYS10 3.4 130.1 1.0 CB J:CYS7 3.4 142.1 1.0 N J:CYS46 3.4 146.1 1.0 N J:GLY11 3.6 129.3 1.0 CB J:CYS46 3.6 159.6 1.0 CD J:ARG43 3.6 133.9 1.0 CA J:CYS46 3.6 155.8 1.0 C J:CYS45 3.7 131.2 1.0 CB J:CYS45 3.8 144.3 1.0 C J:CYS10 3.9 131.7 1.0 O J:CYS45 3.9 135.2 1.0 CZ J:ARG43 4.0 134.6 1.0 N J:LYS12 4.0 138.5 1.0 NH2 J:ARG43 4.1 139.9 1.0 CB J:LYS12 4.3 131.6 1.0 CG J:ARG43 4.3 130.6 1.0 CA J:CYS45 4.4 132.6 1.0 C J:SER9 4.7 130.3 1.0 CA J:GLY11 4.8 128.3 1.0 CA J:LYS12 4.8 133.0 1.0 CA J:CYS7 4.8 135.7 1.0 C J:GLY11 4.9 133.0 1.0

Zinc binding site 4 out of 4 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Open State


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, Open State within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn3001 b:294.4 occ:1.00 OD1 L:ASP50 2.0 215.8 1.0 SG L:CYS31 2.3 176.2 1.0 SG L:CYS34 2.3 198.9 1.0 SG L:CYS48 2.3 189.4 1.0 SG L:CYS51 2.3 204.5 1.0 CB L:CYS34 2.6 185.5 1.0 CB L:CYS51 2.8 196.7 1.0 N L:CYS34 3.1 181.7 1.0 CG L:ASP50 3.2 209.5 1.0 CB L:CYS31 3.3 170.1 1.0 CA L:CYS34 3.4 181.5 1.0 N L:CYS51 3.6 198.3 1.0 CB L:CYS48 3.7 175.4 1.0 CA L:CYS51 3.8 197.2 1.0 OD2 L:ASP50 3.9 211.6 1.0 OG L:SER36 4.1 155.9 1.0 C L:CYS34 4.1 176.3 1.0 C L:ASP50 4.3 202.4 1.0 CB L:ASP50 4.3 202.0 1.0 C L:GLU33 4.3 168.0 1.0 N L:SER35 4.3 152.0 1.0 CB L:GLU33 4.5 169.9 1.0 CA L:CYS31 4.7 170.1 1.0 CA L:ASP50 4.8 200.0 1.0 CA L:GLU33 4.8 166.4 1.0 C L:CYS51 4.9 194.0 1.0 N L:ASP50 4.9 199.0 1.0 N L:GLU33 4.9 163.9 1.0 O L:CYS34 5.0 176.2 1.0 CG L:GLU33 5.0 171.5 1.0 CA L:CYS48 5.0 177.5 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