Calcium 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
Zinc	(Zn)	5 atoms

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

Calcium binding site 1 out of 2 in the Structure of Tfiih/RAD4-RAD23-RAD33/Dna in Dna Opening


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 E:Ca400 b:62.7 occ:1.00 O E:VAL124 2.4 42.4 1.0 OD2 E:ASP129 2.5 0.0 1.0 CB E:ARG107 3.3 49.6 1.0 CD E:ARG107 3.6 0.0 1.0 CG E:ARG107 3.6 0.0 1.0 C E:VAL124 3.6 35.7 1.0 CG E:ASP129 3.7 0.0 1.0 N E:SER126 4.0 39.0 1.0 CA E:LEU125 4.3 27.6 1.0 OG E:SER126 4.4 0.0 1.0 N E:LEU125 4.4 27.3 1.0 OD1 E:ASP129 4.5 0.0 1.0 CB E:SER126 4.6 49.0 1.0 C E:LEU125 4.6 31.1 1.0 CB E:ASP129 4.6 30.8 1.0 CA E:VAL124 4.7 26.8 1.0 CA E:ARG107 4.8 42.9 1.0 N E:VAL124 4.8 29.2 1.0 CA E:SER126 4.9 43.0 1.0 CB E:VAL124 4.9 34.5 1.0 N E:ASN108 4.9 39.8 1.0 NE E:ARG107 5.0 0.0 1.0 N E:CYS109 5.0 41.9 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 E:Ca401 b:41.4 occ:1.00 O E:PHE159 2.6 41.5 1.0 OD2 E:ASP164 3.2 0.0 1.0 CG2 E:THR153 3.5 0.0 1.0 C E:PHE159 3.7 34.9 1.0 N E:GLY155 4.0 46.3 1.0 N E:ARG157 4.1 50.0 1.0 CA E:THR153 4.2 51.3 1.0 N E:ASP154 4.2 46.5 1.0 N E:LYS156 4.3 52.5 1.0 CB E:THR153 4.4 55.1 1.0 CA E:MET160 4.4 33.9 1.0 N E:THR161 4.4 35.7 1.0 N E:MET160 4.4 35.5 1.0 CB E:ARG157 4.4 29.7 1.0 N E:PHE159 4.4 35.8 1.0 CG E:ASP164 4.5 0.0 1.0 C E:THR153 4.5 57.8 1.0 CG2 E:THR161 4.5 0.0 1.0 CA E:GLY155 4.5 68.6 1.0 CA E:PHE159 4.6 34.1 1.0 C E:GLY155 4.7 64.6 1.0 OG1 E:THR161 4.7 0.0 1.0 OG1 E:THR153 4.8 0.0 1.0 CA E:ARG157 4.8 37.8 1.0 C E:MET160 4.9 32.9 1.0 CG E:ARG157 5.0 0.0 1.0 C E:ASP154 5.0 65.2 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