Zinc in PDB 7ob9: Cryo-Em Structure of Human Rna Polymerase I in Elongation State

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase I in Elongation State:
2.7.7.6;

The structure of Cryo-Em Structure of Human Rna Polymerase I in Elongation State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State (pdb code 7ob9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State, PDB code: 7ob9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:100.6 occ:1.00 NE2 A:HIS77 2.2 63.3 1.0 SG A:CYS74 2.4 74.6 1.0 SG A:CYS67 2.4 83.9 1.0 CD2 A:HIS77 2.4 63.3 1.0 SG A:CYS64 2.4 83.1 1.0 CB A:CYS64 3.2 83.1 1.0 OG1 A:THR66 3.4 80.1 1.0 CE1 A:HIS77 3.4 63.3 1.0 CG A:HIS77 3.8 63.3 1.0 CB A:CYS67 3.8 83.9 1.0 CB A:CYS74 3.9 74.6 1.0 N A:CYS67 3.9 83.9 1.0 ND1 A:HIS77 4.2 63.3 1.0 CA A:CYS67 4.3 83.9 1.0 O A:LEU55 4.4 64.3 1.0 CA A:CYS74 4.6 74.6 1.0 CA A:CYS64 4.7 83.1 1.0 O A:CYS67 4.7 83.9 1.0 C A:CYS67 4.7 83.9 1.0 CB A:THR66 4.8 80.1 1.0 CA A:GLY56 4.8 66.9 1.0 N A:GLY76 4.9 64.0 1.0 C A:LEU55 4.9 64.3 1.0 CB A:HIS77 5.0 63.3 1.0 C A:THR66 5.0 80.1 1.0 N A:THR66 5.0 80.1 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:127.5 occ:1.00 SG A:CYS107 2.4 90.1 1.0 SG A:CYS104 2.4 82.2 1.0 SG A:CYS205 2.5 101.6 1.0 SG A:CYS208 2.5 106.0 1.0 CB A:CYS104 3.1 82.2 1.0 CB A:CYS107 3.2 90.1 1.0 CB A:CYS205 3.4 101.6 1.0 CB A:CYS208 3.4 106.0 1.0 N A:CYS107 3.5 90.1 1.0 N A:CYS208 3.9 106.0 1.0 CA A:CYS107 3.9 90.1 1.0 CA A:CYS208 4.3 106.0 1.0 CB A:ASN106 4.4 87.8 1.0 C A:ASN106 4.6 87.8 1.0 CA A:CYS104 4.6 82.2 1.0 CB A:HIS207 4.6 103.7 1.0 C A:CYS107 4.7 90.1 1.0 N A:ASN106 4.7 87.8 1.0 OG1 A:THR210 4.7 104.8 1.0 CA A:ASN106 4.8 87.8 1.0 N A:HIS108 4.8 82.7 1.0 CA A:CYS205 4.8 101.6 1.0 C A:HIS207 4.9 103.7 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:110.8 occ:1.00 SG B:CYS1098 2.4 75.5 1.0 SG B:CYS1070 2.5 69.1 1.0 SG B:CYS1101 2.5 85.5 1.0 SG B:CYS1073 2.7 69.6 1.0 CB B:CYS1101 3.4 85.5 1.0 CB B:CYS1098 3.4 75.5 1.0 CB B:CYS1073 3.4 69.6 1.0 CB B:CYS1070 3.6 69.1 1.0 N B:CYS1101 3.8 85.5 1.0 N B:CYS1073 3.9 69.6 1.0 CA B:CYS1101 4.2 85.5 1.0 OG1 B:THR1106 4.3 77.0 1.0 CA B:CYS1073 4.3 69.6 1.0 CB B:LYS1072 4.4 71.7 1.0 CB B:LEU1100 4.5 75.3 1.0 OG B:SER1078 4.6 63.4 1.0 CD B:LYS1072 4.8 71.7 1.0 CA B:CYS1098 4.8 75.5 1.0 CG B:LYS1072 4.8 71.7 1.0 C B:LEU1100 4.9 75.3 1.0 C B:LYS1072 4.9 71.7 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:132.2 occ:1.00 SG I:CYS38 2.4 91.5 1.0 SG I:CYS20 2.4 78.4 1.0 SG I:CYS23 2.4 81.4 1.0 SG I:CYS41 2.4 90.8 1.0 CB I:CYS20 2.8 78.4 1.0 CB I:CYS38 3.1 91.5 1.0 CB I:CYS41 3.6 90.8 1.0 CB I:CYS23 3.7 81.4 1.0 N I:CYS23 3.8 81.4 1.0 N I:CYS41 4.2 90.8 1.0 CA I:CYS23 4.2 81.4 1.0 CA I:CYS20 4.3 78.4 1.0 CA I:CYS41 4.4 90.8 1.0 CB I:SER25 4.5 70.3 1.0 CA I:CYS38 4.6 91.5 1.0 N I:SER25 4.6 70.3 1.0 C I:CYS23 4.7 81.4 1.0 C I:CYS20 4.7 78.4 1.0 N I:GLY24 4.7 72.1 1.0 CB I:ASP22 4.8 87.8 1.0 C I:ASP22 4.8 87.8 1.0 N I:ASP22 4.8 87.8 1.0 CB I:PHE43 5.0 94.8 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:54.7 occ:1.00 SG J:CYS10 2.4 32.9 1.0 SG J:CYS44 2.4 35.2 1.0 SG J:CYS45 2.4 37.1 1.0 SG J:CYS7 2.5 33.6 1.0 N J:CYS45 3.0 37.1 1.0 CB J:CYS7 3.2 33.6 1.0 CA J:CYS45 3.3 37.1 1.0 CB J:CYS45 3.5 37.1 1.0 C J:CYS44 3.6 35.2 1.0 CB J:CYS44 3.7 35.2 1.0 CB J:CYS10 3.8 32.9 1.0 N J:CYS10 3.8 32.9 1.0 O J:CYS10 4.0 32.9 1.0 O J:CYS44 4.2 35.2 1.0 CA J:CYS10 4.2 32.9 1.0 CA J:CYS44 4.3 35.2 1.0 C J:CYS10 4.4 32.9 1.0 NE J:ARG42 4.5 33.8 1.0 CB J:LYS12 4.5 33.2 1.0 NH2 J:ARG42 4.5 33.8 1.0 CA J:CYS7 4.6 33.6 1.0 CB J:THR9 4.8 32.4 1.0 C J:CYS45 4.8 37.1 1.0 C J:THR9 4.9 32.4 1.0 N J:LYS12 5.0 33.2 1.0 N J:THR9 5.0 32.4 1.0 CZ J:ARG42 5.0 33.8 1.0 N J:CYS44 5.0 35.2 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Human Rna Polymerase I in Elongation State


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 Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:78.4 occ:1.00 SG L:CYS36 2.4 59.3 1.0 SG L:CYS39 2.4 61.1 1.0 SG L:CYS22 2.4 62.8 1.0 SG L:CYS19 2.4 57.3 1.0 CB L:CYS36 2.8 59.3 1.0 CB L:CYS19 2.9 57.3 1.0 CB L:CYS22 3.7 62.8 1.0 CB L:CYS39 3.8 61.1 1.0 N L:CYS39 3.9 61.1 1.0 OG1 L:THR24 4.1 62.4 1.0 N L:CYS22 4.1 62.8 1.0 CA L:CYS39 4.3 61.1 1.0 CA L:CYS36 4.3 59.3 1.0 CB L:TYR41 4.4 51.8 1.0 CA L:CYS19 4.4 57.3 1.0 CA L:CYS22 4.5 62.8 1.0 N L:TYR41 4.6 51.8 1.0 N L:GLY40 4.6 56.5 1.0 C L:CYS39 4.7 61.1 1.0 C L:CYS36 4.9 59.3 1.0 CB L:GLU38 4.9 65.4 1.0 N L:HIS23 5.0 65.4 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