Zinc in PDB 7k01: Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex

Enzymatic activity of Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex

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

Other elements in 7k01:

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

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex (pdb code 7k01). 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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex, PDB code: 7k01:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7k01

Go back to Zinc Binding Sites List in 7k01
Zinc binding site 1 out of 5 in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex


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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex 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 7k01

Go back to Zinc Binding Sites List in 7k01
Zinc binding site 2 out of 5 in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex


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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn501

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 4.4 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 7k01

Go back to Zinc Binding Sites List in 7k01
Zinc binding site 3 out of 5 in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex


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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn502

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 7k01

Go back to Zinc Binding Sites List in 7k01
Zinc binding site 4 out of 5 in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex


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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn503

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 7k01

Go back to Zinc Binding Sites List in 7k01
Zinc binding site 5 out of 5 in the Structure of Tfiih in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex


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 in Tfiih/RAD4-RAD23-RAD33 Dna Opening Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn504

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

Reference:

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
Page generated: Sun Aug 22 09:46:25 2021

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