Zinc in PDB 7k04: Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening

All present enzymatic activity of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening:
3.6.4.12;

The structure of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening (pdb code 7k04). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening, PDB code: 7k04:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn401 b:0.0 occ:1.00 CB 4:CYS292 1.4 0.0 1.0 SG 4:CYS305 2.3 0.0 1.0 SG 4:CYS292 2.3 0.0 1.0 SG 4:CYS308 2.3 0.0 1.0 SG 4:CYS289 2.3 0.0 1.0 CA 4:CYS292 2.9 0.0 1.0 CB 4:CYS308 3.4 0.0 1.0 N 4:CYS292 3.5 0.0 1.0 CB 4:CYS289 3.7 0.0 1.0 C 4:CYS292 3.8 0.0 1.0 CB 4:CYS305 3.9 0.0 1.0 N 4:CYS308 3.9 0.0 1.0 CA 4:CYS308 4.2 0.0 1.0 N 4:LEU293 4.2 0.0 1.0 O 4:CYS308 4.2 0.0 1.0 C 4:CYS308 4.6 0.0 1.0 O 4:CYS292 4.7 0.0 1.0 N 4:SER290 4.7 0.0 1.0 N 4:CYS294 4.8 0.0 1.0 C 4:VAL291 4.8 0.0 1.0 O 4:CYS305 4.8 0.0 1.0 C 4:ALA307 4.8 0.0 1.0

Zinc binding site 2 out of 5 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn462 b:0.0 occ:1.00 SG 6:CYS440 2.3 0.0 1.0 SG 6:CYS403 2.3 0.0 1.0 SG 6:CYS406 2.3 0.0 1.0 SG 6:CYS437 2.3 0.0 1.0 CB 6:CYS406 2.8 0.0 1.0 CB 6:CYS403 2.9 0.0 1.0 CB 6:CYS440 3.3 0.0 1.0 N 6:CYS406 3.6 0.0 1.0 CA 6:CYS406 3.6 0.0 1.0 CB 6:CYS437 3.9 0.0 1.0 C 6:CYS406 3.9 0.0 1.0 N 6:CYS437 4.0 0.0 1.0 CB 6:SER408 4.2 0.0 1.0 CA 6:CYS403 4.3 0.0 1.0 O 6:CYS406 4.3 0.0 1.0 CA 6:CYS440 4.4 0.0 1.0 N 6:CYS440 4.5 0.0 1.0 N 6:GLN407 4.5 0.0 1.0 N 6:SER408 4.5 0.0 1.0 CA 6:CYS437 4.5 0.0 1.0 C 6:SER405 4.8 0.0 1.0 N 6:PHE404 4.8 0.0 1.0 N 6:SER405 5.0 0.0 1.0

Zinc binding site 3 out of 5 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn463 b:0.0 occ:1.00 SG 6:CYS454 2.3 0.0 1.0 SG 6:CYS432 2.3 0.0 1.0 SG 6:CYS451 2.3 0.0 1.0 SG 6:CYS429 2.3 0.0 1.0 CB 6:CYS432 2.9 0.0 1.0 CB 6:CYS454 3.1 0.0 1.0 N 6:CYS432 3.4 0.0 1.0 CB 6:CYS429 3.5 0.0 1.0 N 6:CYS454 3.6 0.0 1.0 CA 6:CYS432 3.7 0.0 1.0 CB 6:CYS451 3.8 0.0 1.0 CA 6:CYS454 3.8 0.0 1.0 C 6:CYS432 4.6 0.0 1.0 C 6:ASP431 4.6 0.0 1.0 C 6:GLY453 4.6 0.0 1.0 N 6:LYS433 4.7 0.0 1.0 N 6:ASP431 4.7 0.0 1.0 CA 6:CYS429 4.7 0.0 1.0 C 6:CYS429 4.8 0.0 1.0 N 6:GLU430 5.0 0.0 1.0 CA 6:GLY453 5.0 0.0 1.0

Zinc binding site 4 out of 5 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn464 b:0.0 occ:1.00 CB 6:CYS352 1.8 0.0 1.0 SG 6:CYS363 2.3 0.0 1.0 SG 6:CYS366 2.3 0.0 1.0 SG 6:CYS349 2.3 0.0 1.0 SG 6:CYS352 2.3 0.0 1.0 CB 6:CYS349 2.9 0.0 1.0 CB 6:CYS363 3.1 0.0 1.0 CA 6:CYS352 3.1 0.0 1.0 N 6:CYS352 3.3 0.0 1.0 N 6:CYS366 3.7 0.0 1.0 CB 6:CYS366 3.7 0.0 1.0 C 6:CYS352 4.0 0.0 1.0 N 6:HIS353 4.2 0.0 1.0 CA 6:CYS366 4.2 0.0 1.0 CB 6:CYS365 4.4 0.0 1.0 CA 6:CYS349 4.4 0.0 1.0 CA 6:CYS363 4.5 0.0 1.0 C 6:ASN351 4.6 0.0 1.0 C 6:CYS365 4.7 0.0 1.0 N 6:ASP367 4.7 0.0 1.0 N 6:CYS365 4.8 0.0 1.0 C 6:CYS366 4.8 0.0 1.0 CA 6:CYS365 4.8 0.0 1.0 CD2 6:LEU368 4.8 30.0 1.0 O 6:CYS352 4.9 0.0 1.0 CG 6:LEU368 5.0 30.0 1.0 OG 6:SER354 5.0 30.0 1.0 C 6:CYS363 5.0 0.0 1.0 C 6:CYS349 5.0 0.0 1.0

Zinc binding site 5 out of 5 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn465 b:0.0 occ:1.00 ND1 6:HIS339 2.0 30.0 1.0 SG 6:CYS338 2.3 30.0 1.0 SG 6:CYS336 2.3 30.0 1.0 SG 6:CYS357 2.3 30.0 1.0 CG 6:HIS339 2.9 30.0 1.0 CE1 6:HIS339 3.0 30.0 1.0 N 6:HIS339 3.0 0.0 1.0 CB 6:CYS357 3.1 30.0 1.0 CB 6:HIS339 3.3 30.0 1.0 CB 6:CYS336 3.4 30.0 1.0 C 6:CYS338 3.6 0.0 1.0 CB 6:CYS338 3.7 30.0 1.0 CA 6:HIS339 3.7 0.0 1.0 N 6:CYS338 3.7 0.0 1.0 N 6:CYS357 3.8 0.0 1.0 CA 6:CYS338 3.8 0.0 1.0 CA 6:CYS357 4.0 0.0 1.0 NE2 6:HIS339 4.0 30.0 1.0 CD2 6:HIS339 4.0 30.0 1.0 O 6:CYS338 4.4 0.0 1.0 CA 6:CYS336 4.5 0.0 1.0 C 6:HIS339 4.6 0.0 1.0 N 6:SER337 4.7 0.0 1.0 N 6:SER340 4.7 0.0 1.0 C 6:CYS336 4.8 0.0 1.0 C 6:VAL356 4.9 0.0 1.0 C 6:SER337 5.0 0.0 1.0

T.Van Eeuwen, Y.Shim, H.J.Kim, T.Zhao, S.Basu, B.A.Garcia, C.D.Kaplan, J.H.Min, K.Murakami. Cryo-Em Structure of Tfiih/RAD4-RAD23-RAD33 in Damaged Dna Opening in Nucleotide Excision Repair. Nat Commun V. 12 3338 2021.
ISSN: ESSN 2041-1723
PubMed: 34099686
DOI: 10.1038/S41467-021-23684-X