Zinc in PDB 8hyj: A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex

All present enzymatic activity of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex:
2.7.7.6;

The structure of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex (pdb code 8hyj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex, PDB code: 8hyj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:114.2 occ:1.00 SG C:CYS99 2.3 80.9 1.0 SG C:CYS93 2.3 106.0 1.0 SG C:CYS90 2.3 95.5 1.0 SG C:CYS102 2.3 77.7 1.0 CB C:CYS99 3.1 80.9 1.0 CB C:CYS93 3.3 106.0 1.0 CB C:CYS90 3.3 95.5 1.0 CB C:CYS102 3.4 77.7 1.0 N C:CYS102 4.0 77.7 1.0 N C:CYS93 4.2 106.0 1.0 CA C:CYS102 4.3 77.7 1.0 CA C:CYS93 4.4 106.0 1.0 CA C:CYS99 4.5 80.9 1.0 C C:ASP92 4.5 102.0 1.0 CB C:ASP92 4.6 102.0 1.0 O C:CYS90 4.6 95.5 1.0 CA C:CYS90 4.7 95.5 1.0 CB C:PHE101 4.7 80.1 1.0 N C:ASP92 4.7 102.0 1.0 C C:CYS90 4.8 95.5 1.0 CA C:ASP92 4.9 102.0 1.0 O C:ASP92 4.9 102.0 1.0 C C:CYS102 5.0 77.7 1.0

Zinc binding site 2 out of 4 in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:120.1 occ:1.00 SG I:CYS10 2.3 99.0 1.0 SG I:CYS32 2.3 116.7 1.0 SG I:CYS7 2.4 97.6 1.0 SG I:CYS29 2.4 117.6 1.0 CB I:CYS7 3.4 97.6 1.0 CB I:CYS32 3.4 116.7 1.0 CB I:CYS29 3.5 117.6 1.0 CB I:CYS10 3.6 99.0 1.0 N I:CYS32 4.0 116.7 1.0 OD1 I:ASN12 4.1 97.1 1.0 CA I:CYS32 4.1 116.7 1.0 CB I:ASN12 4.2 97.1 1.0 N I:ASP33 4.4 119.1 1.0 N I:CYS10 4.4 99.0 1.0 C I:CYS32 4.5 116.7 1.0 CG I:ASN12 4.5 97.1 1.0 CA I:CYS10 4.6 99.0 1.0 CA I:CYS7 4.8 97.6 1.0 CA I:CYS29 4.9 117.6 1.0

Zinc binding site 3 out of 4 in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn200 b:68.5 occ:1.00 SG J:CYS10 2.3 51.1 1.0 SG J:CYS45 2.3 54.1 1.0 SG J:CYS7 2.3 47.8 1.0 SG J:CYS44 2.3 53.9 1.0 CB J:CYS10 3.2 51.1 1.0 O J:CYS10 3.3 51.1 1.0 CB J:CYS7 3.3 47.8 1.0 N J:CYS10 3.5 51.1 1.0 CB J:CYS44 3.5 53.9 1.0 CB J:CYS45 3.5 54.1 1.0 CA J:CYS10 3.8 51.1 1.0 C J:CYS44 3.8 53.9 1.0 C J:CYS10 3.8 51.1 1.0 O J:CYS44 3.9 53.9 1.0 CA J:CYS45 3.9 54.1 1.0 N J:CYS45 4.0 54.1 1.0 CA J:CYS44 4.3 53.9 1.0 NE J:ARG42 4.5 50.1 1.0 NH2 J:ARG42 4.6 50.1 1.0 CB J:THR9 4.6 48.6 1.0 C J:THR9 4.7 48.6 1.0 CA J:CYS7 4.7 47.8 1.0 N J:LYS12 4.8 47.2 1.0 CB J:LYS12 4.8 47.2 1.0 N J:CYS44 4.8 53.9 1.0 N J:THR9 4.9 48.6 1.0 C J:CYS7 5.0 47.8 1.0 N J:GLY11 5.0 47.0 1.0 CA J:THR9 5.0 48.6 1.0

Zinc binding site 4 out of 4 in the A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:100.6 occ:1.00 SG L:CYS15 2.3 85.2 1.0 SG L:CYS32 2.3 84.1 1.0 SG L:CYS29 2.4 78.7 1.0 SG L:CYS12 2.4 72.9 1.0 CB L:CYS15 3.4 85.2 1.0 CB L:CYS12 3.4 72.9 1.0 CB L:CYS32 3.4 84.1 1.0 CB L:CYS29 3.4 78.7 1.0 OD2 L:ASP14 4.1 80.9 1.0 N L:CYS32 4.1 84.1 1.0 N L:CYS15 4.1 85.2 1.0 O L:CYS15 4.2 85.2 1.0 OD1 L:ASP14 4.2 80.9 1.0 CA L:CYS15 4.2 85.2 1.0 CA L:CYS32 4.3 84.1 1.0 C L:CYS15 4.4 85.2 1.0 CG L:ASP14 4.4 80.9 1.0 CB L:GLN17 4.5 83.7 1.0 CG L:GLN17 4.8 83.7 1.0 CA L:CYS12 4.9 72.9 1.0 CA L:CYS29 4.9 78.7 1.0 CB L:GLU31 5.0 79.1 1.0 C L:ASP14 5.0 80.9 1.0

H.W.Zhang, K.Huang, Z.X.Gu, X.X.Wu, J.W.Wang, Y.Zhang. A Cryo-Em Structure of KTF1-Bound Polymerase V Transcription Elongation Complex. Nat Commun V. 14 3118 2023.
ISSN: ESSN 2041-1723
PubMed: 37253723
DOI: 10.1038/S41467-023-38619-X