Zinc in PDB 7oba: Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3:
2.7.7.6;

The binding sites of Zinc atom in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 (pdb code 7oba). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3, PDB code: 7oba:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:98.3 occ:1.00 NE2 A:HIS77 2.2 89.1 1.0 SG A:CYS74 2.5 89.1 1.0 SG A:CYS67 2.5 98.2 1.0 CD2 A:HIS77 2.8 89.1 1.0 SG A:CYS64 2.8 98.1 1.0 CB A:CYS64 3.2 98.1 1.0 O A:CYS67 3.3 98.2 1.0 CE1 A:HIS77 3.3 89.1 1.0 CB A:CYS74 3.7 89.1 1.0 N A:CYS67 3.8 98.2 1.0 CB A:CYS67 3.8 98.2 1.0 CG A:HIS77 4.1 89.1 1.0 CA A:CYS67 4.1 98.2 1.0 C A:CYS67 4.1 98.2 1.0 ND1 A:HIS77 4.3 89.1 1.0 CA A:CYS64 4.7 98.1 1.0 CB A:THR66 4.8 96.2 1.0 C A:THR66 4.9 96.2 1.0 N A:GLY76 4.9 85.5 1.0 CA A:CYS74 4.9 89.1 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:130.7 occ:1.00 SG A:CYS104 2.5 108.0 1.0 SG A:CYS107 2.5 112.0 1.0 SG A:CYS205 2.5 114.5 1.0 CB A:CYS208 3.1 119.5 1.0 N A:CYS107 3.2 112.0 1.0 CB A:CYS107 3.6 112.0 1.0 CB A:CYS205 3.6 114.5 1.0 O A:CYS107 3.8 112.0 1.0 CB A:ASN106 3.8 115.1 1.0 CA A:CYS107 3.8 112.0 1.0 CB A:CYS104 4.0 108.0 1.0 SG A:CYS208 4.1 119.5 1.0 C A:ASN106 4.2 115.1 1.0 N A:CYS208 4.3 119.5 1.0 C A:CYS107 4.3 112.0 1.0 CA A:CYS208 4.3 119.5 1.0 CA A:ASN106 4.4 115.1 1.0 N A:ASN106 4.5 115.1 1.0 OG1 A:THR210 4.8 118.0 1.0 OD1 A:ASN106 4.8 115.1 1.0 CG A:ASN106 4.8 115.1 1.0 CA A:CYS205 5.0 114.5 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:105.8 occ:1.00 SG B:CYS1070 2.5 84.6 1.0 SG B:CYS1073 2.5 86.2 1.0 SG B:CYS1098 2.8 90.8 1.0 CB B:CYS1073 2.9 86.2 1.0 CB B:CYS1070 3.1 84.6 1.0 SG B:CYS1101 3.6 93.0 1.0 N B:CYS1073 3.7 86.2 1.0 CA B:CYS1073 3.9 86.2 1.0 CB B:CYS1098 4.1 90.8 1.0 O B:CYS1070 4.4 84.6 1.0 CB B:CYS1101 4.4 93.0 1.0 CE B:LYS1072 4.5 87.5 1.0 NZ B:LYS1072 4.5 87.5 1.0 CA B:CYS1070 4.5 84.6 1.0 CD2 B:LEU1100 4.7 89.7 1.0 C B:CYS1070 4.7 84.6 1.0 N B:GLY1074 4.8 80.0 1.0 C B:LYS1072 4.9 87.5 1.0 CB B:LYS1072 4.9 87.5 1.0 C B:CYS1073 4.9 86.2 1.0 CB B:LEU1100 5.0 89.7 1.0 OG B:SER1078 5.0 79.9 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:80.7 occ:1.00 SG I:CYS20 2.4 66.4 1.0 SG I:CYS38 2.5 77.6 1.0 CB I:CYS20 2.6 66.4 1.0 CB I:CYS38 2.6 77.6 1.0 SG I:CYS41 2.6 78.8 1.0 SG I:CYS23 2.8 71.1 1.0 CA I:CYS20 4.0 66.4 1.0 CA I:CYS38 4.1 77.6 1.0 CB I:CYS41 4.1 78.8 1.0 CB I:CYS23 4.4 71.1 1.0 N I:CYS23 4.6 71.1 1.0 N I:CYS41 4.6 78.8 1.0 CB I:PHE43 4.7 78.0 1.0 O I:PHE43 4.7 78.0 1.0 CD2 I:LEU27 4.7 63.3 1.0 N I:CYS20 4.8 66.4 1.0 N I:CYS38 4.8 77.6 1.0 CA I:CYS41 4.9 78.8 1.0 C I:CYS20 4.9 66.4 1.0 CA I:CYS23 5.0 71.1 1.0 C I:CYS38 5.0 77.6 1.0 CB I:SER25 5.0 59.7 1.0 N I:PHE43 5.0 78.0 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:104.6 occ:1.00 SG I:CYS87 2.4 73.8 1.0 SG I:CYS118 2.5 72.5 1.0 SG I:CYS90 2.5 82.4 1.0 SG I:CYS115 2.5 62.2 1.0 CB I:CYS115 3.0 62.2 1.0 CB I:CYS87 3.0 73.8 1.0 CB I:CYS118 3.7 72.5 1.0 N I:CYS118 3.8 72.5 1.0 CB I:CYS90 3.9 82.4 1.0 N I:CYS90 4.3 82.4 1.0 CA I:CYS118 4.3 72.5 1.0 CB I:HIS92 4.5 75.7 1.0 CA I:CYS115 4.5 62.2 1.0 CA I:CYS87 4.5 73.8 1.0 CA I:CYS90 4.6 82.4 1.0 N I:LYS119 4.7 66.6 1.0 C I:CYS118 4.7 72.5 1.0 N I:HIS92 4.7 75.7 1.0 CB I:PHE120 4.8 63.8 1.0 N I:GLY91 4.9 80.8 1.0 N I:ASN117 4.9 70.4 1.0 CB I:ASN117 4.9 70.4 1.0 N I:PHE120 5.0 63.8 1.0 C I:ASN117 5.0 70.4 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:40.5 occ:1.00 SG J:CYS7 2.4 22.5 1.0 SG J:CYS44 2.4 26.6 1.0 SG J:CYS10 2.5 23.0 1.0 SG J:CYS45 2.5 27.1 1.0 N J:CYS45 3.3 27.1 1.0 CB J:CYS7 3.3 22.5 1.0 O J:CYS10 3.6 23.0 1.0 CA J:CYS45 3.6 27.1 1.0 CB J:CYS45 3.6 27.1 1.0 C J:CYS44 3.6 26.6 1.0 CB J:CYS44 3.7 26.6 1.0 N J:CYS10 3.7 23.0 1.0 CB J:CYS10 3.9 23.0 1.0 O J:CYS44 4.0 26.6 1.0 CA J:CYS10 4.2 23.0 1.0 C J:CYS10 4.2 23.0 1.0 CA J:CYS44 4.2 26.6 1.0 NH2 J:ARG42 4.3 27.1 1.0 NE J:ARG42 4.5 27.1 1.0 CB J:THR9 4.5 23.6 1.0 CA J:CYS7 4.7 22.5 1.0 C J:THR9 4.8 23.6 1.0 N J:CYS44 4.9 26.6 1.0 CB J:LYS12 4.9 23.7 1.0 CZ J:ARG42 4.9 27.1 1.0 N J:THR9 5.0 23.6 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human Rna Polymerase I in Complex with RRN3 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:56.2 occ:1.00 SG L:CYS22 2.4 46.0 1.0 SG L:CYS36 2.4 45.3 1.0 SG L:CYS19 2.5 42.2 1.0 SG L:CYS39 2.5 46.0 1.0 CB L:CYS36 2.7 45.3 1.0 CB L:CYS19 3.0 42.2 1.0 CB L:CYS22 3.8 46.0 1.0 CB L:CYS39 3.9 46.0 1.0 N L:CYS39 4.0 46.0 1.0 CA L:CYS36 4.2 45.3 1.0 OG1 L:THR24 4.2 44.3 1.0 N L:GLY40 4.3 42.6 1.0 N L:CYS22 4.3 46.0 1.0 N L:TYR41 4.3 39.3 1.0 CA L:CYS39 4.4 46.0 1.0 CB L:TYR41 4.4 39.3 1.0 CA L:CYS19 4.5 42.2 1.0 CA L:CYS22 4.6 46.0 1.0 C L:CYS36 4.8 45.3 1.0 C L:CYS39 4.8 46.0 1.0 N L:HIS23 4.9 42.9 1.0 O L:TYR41 4.9 39.3 1.0 CA L:TYR41 5.0 39.3 1.0 C L:CYS22 5.0 46.0 1.0

A.D.Misiaszek, M.Girbig, C.W.Mueller. Cryo-Em Structures of Human Rna Polymerase I. To Be Published.
DOI: 10.1038/S41594-021-00693-4