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

Enzymatic activity of 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;

Other elements in 8hyj:

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

Zinc Binding Sites:

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 8hyj

Go back to Zinc Binding Sites List in 8hyj
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 8hyj

Go back to Zinc Binding Sites List in 8hyj
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 8hyj

Go back to Zinc Binding Sites List in 8hyj
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 8hyj

Go back to Zinc Binding Sites List in 8hyj
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

Reference:

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
Page generated: Fri Jul 28 07:09:58 2023

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