Iron 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:

Calcium	(Ca)	2 atoms
Zinc	(Zn)	5 atoms

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening, PDB code: 7k04:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 0:Fe801 b:0.0 occ:1.00 FE1 0:SF4801 0.0 0.0 1.0 SG 0:CYS115 2.2 117.6 1.0 S3 0:SF4801 2.3 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 S4 0:SF4801 2.3 0.0 1.0 CB 0:CYS115 2.6 117.6 1.0 CA 0:CYS115 2.7 117.6 1.0 FE2 0:SF4801 2.7 0.0 1.0 FE4 0:SF4801 2.7 0.0 1.0 FE3 0:SF4801 2.7 0.0 1.0 N 0:LEU116 3.5 100.9 1.0 C 0:CYS115 3.5 117.6 1.0 N 0:CYS115 3.8 117.6 1.0 S1 0:SF4801 3.9 0.0 1.0 N 0:HIS117 4.4 89.3 1.0 C 0:LEU114 4.6 146.6 1.0 O 0:LEU114 4.6 146.6 1.0 O 0:CYS115 4.6 117.6 1.0 CB 0:CYS191 4.7 115.3 1.0 SG 0:CYS133 4.8 46.6 1.0 CA 0:LEU116 4.8 100.9 1.0 SG 0:CYS156 4.8 90.8 1.0 CB 0:TYR193 4.9 84.4 1.0 CB 0:HIS117 5.0 89.3 1.0

Iron binding site 2 out of 4 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 0:Fe801 b:0.0 occ:1.00 FE2 0:SF4801 0.0 0.0 1.0 SG 0:CYS156 2.2 90.8 1.0 S4 0:SF4801 2.3 0.0 1.0 S3 0:SF4801 2.3 0.0 1.0 S1 0:SF4801 2.3 0.0 1.0 SG 0:CYS115 2.4 117.6 1.0 FE1 0:SF4801 2.7 0.0 1.0 FE3 0:SF4801 2.7 0.0 1.0 FE4 0:SF4801 2.7 0.0 1.0 CB 0:HIS117 3.1 89.3 1.0 CB 0:CYS156 3.5 90.8 1.0 S2 0:SF4801 3.9 0.0 1.0 N 0:HIS117 4.0 89.3 1.0 CG 0:HIS117 4.1 89.3 1.0 CB 0:CYS115 4.1 117.6 1.0 CA 0:HIS117 4.1 89.3 1.0 CG1 0:VAL120 4.5 54.5 1.0 CB 0:VAL120 4.5 54.5 1.0 CD2 0:HIS117 4.5 89.3 1.0 SG 0:CYS133 4.6 46.6 1.0 CG2 0:VAL120 4.6 54.5 1.0 CA 0:CYS115 4.7 117.6 1.0 CD2 0:TYR158 4.7 101.9 1.0 N 0:LEU116 4.7 100.9 1.0 CB 0:CYS133 4.8 46.6 1.0 CA 0:CYS156 4.8 90.8 1.0 C 0:CYS115 5.0 117.6 1.0

Iron binding site 3 out of 4 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 0:Fe801 b:0.0 occ:1.00 FE3 0:SF4801 0.0 0.0 1.0 SG 0:CYS133 2.2 46.6 1.0 S1 0:SF4801 2.3 0.0 1.0 S4 0:SF4801 2.3 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 FE4 0:SF4801 2.7 0.0 1.0 FE2 0:SF4801 2.7 0.0 1.0 FE1 0:SF4801 2.7 0.0 1.0 CB 0:CYS133 3.2 46.6 1.0 CE2 0:PHE194 3.6 83.2 1.0 SG 0:CYS115 3.6 117.6 1.0 S3 0:SF4801 3.9 0.0 1.0 SG 0:CYS156 3.9 90.8 1.0 CA 0:CYS133 4.2 46.6 1.0 CD2 0:PHE194 4.4 83.2 1.0 CZ 0:PHE194 4.4 83.2 1.0 CB 0:CYS115 4.6 117.6 1.0 CB 0:CYS156 4.9 90.8 1.0 CD 0:ARG111 4.9 123.3 1.0 NE 0:ARG111 4.9 123.3 1.0 O 0:CYS133 4.9 46.6 1.0 C 0:CYS133 5.0 46.6 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 0:Fe801 b:0.0 occ:1.00 FE4 0:SF4801 0.0 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 S1 0:SF4801 2.3 0.0 1.0 S3 0:SF4801 2.3 0.0 1.0 FE3 0:SF4801 2.7 0.0 1.0 FE1 0:SF4801 2.7 0.0 1.0 FE2 0:SF4801 2.7 0.0 1.0 CB 0:CYS191 3.0 115.3 1.0 SG 0:CYS156 3.6 90.8 1.0 CB 0:CYS156 3.7 90.8 1.0 S4 0:SF4801 3.9 0.0 1.0 CB 0:TYR158 3.9 101.9 1.0 CA 0:CYS191 3.9 115.3 1.0 CD2 0:TYR158 4.1 101.9 1.0 SG 0:CYS115 4.2 117.6 1.0 SG 0:CYS191 4.3 115.3 1.0 CG 0:TYR158 4.4 101.9 1.0 CE2 0:PHE194 4.4 83.2 1.0 CD2 0:PHE194 4.5 83.2 1.0 N 0:HIS159 4.6 57.3 1.0 SG 0:CYS133 4.8 46.6 1.0 C 0:CYS191 4.9 115.3 1.0 N 0:CYS191 5.0 115.3 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