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

Enzymatic activity of 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;

Other elements in 7k04:

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

Zinc Binding Sites:

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 7k04

Go back to Zinc Binding Sites List in 7k04
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 7k04

Go back to Zinc Binding Sites List in 7k04
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 7k04

Go back to Zinc Binding Sites List in 7k04
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 7k04

Go back to Zinc Binding Sites List in 7k04
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 7k04

Go back to Zinc Binding Sites List in 7k04
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

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 09:46:27 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy