Zinc in PDB 7xv9: Crystal Structure of the Human TR4 Dna-Binding Domain

The structure of Crystal Structure of the Human TR4 Dna-Binding Domain, PDB code: 7xv9 was solved by Y.Liu, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.03 / 1.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	32.229, 32.229, 128.043, 90, 90, 90
R / Rfree (%)	17.6 / 18.1

The binding sites of Zinc atom in the Crystal Structure of the Human TR4 Dna-Binding Domain (pdb code 7xv9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Human TR4 Dna-Binding Domain, PDB code: 7xv9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human TR4 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:10.6 occ:1.00 SG A:CYS120 2.3 10.2 1.0 SG A:CYS137 2.3 9.4 1.0 SG A:CYS117 2.4 9.8 1.0 SG A:CYS134 2.4 10.8 1.0 CB A:CYS117 3.2 10.4 1.0 CB A:CYS137 3.3 8.8 1.0 CB A:CYS120 3.3 9.7 1.0 CB A:CYS134 3.6 10.5 1.0 N A:CYS120 3.7 9.7 1.0 N A:CYS134 4.0 9.7 1.0 CA A:CYS120 4.1 10.0 1.0 CD A:ARG166 4.1 30.8 1.0 N A:CYS137 4.2 9.4 1.0 NH1 A:ARG166 4.2 33.6 1.0 CA A:CYS137 4.3 9.1 1.0 CA A:CYS134 4.3 10.0 1.0 CB A:VAL119 4.4 11.0 1.0 C A:VAL119 4.7 10.8 1.0 CA A:CYS117 4.7 10.9 1.0 CB A:ASP122 4.7 16.3 1.0 C A:CYS120 4.8 9.7 1.0 N A:GLY121 4.8 10.5 1.0 NE A:ARG166 4.9 31.6 1.0 C A:CYS134 4.9 10.3 1.0 CA A:VAL119 4.9 10.4 1.0 N A:ASP122 5.0 11.8 1.0 CZ A:ARG166 5.0 35.5 1.0 O A:CYS134 5.0 10.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human TR4 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:17.1 occ:1.00 SG A:CYS169 2.2 14.7 1.0 SG A:CYS153 2.2 15.4 1.0 SG A:CYS159 2.3 15.7 1.0 SG A:CYS172 2.4 15.5 1.0 CB A:CYS169 3.2 15.3 1.0 CB A:CYS153 3.2 15.5 1.0 CB A:CYS159 3.3 17.8 1.0 CB A:CYS172 3.5 11.8 1.0 CA A:CYS153 4.0 16.2 1.0 O A:HOH342 4.0 26.4 1.0 N A:CYS159 4.1 20.3 1.0 N A:CYS172 4.2 11.2 1.0 CA A:CYS159 4.3 18.2 1.0 CA A:GLN157 4.4 20.9 1.0 CA A:CYS172 4.4 11.1 1.0 N A:ASP158 4.5 22.2 1.0 N A:GLN157 4.6 20.9 1.0 CA A:CYS169 4.6 16.4 1.0 C A:GLN157 4.7 21.5 1.0 C A:CYS153 4.8 20.4 1.0 N A:ARG154 4.9 23.3 1.0 CD1 A:PHE171 4.9 10.5 1.0 N A:SER155 5.0 23.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human TR4 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:10.4 occ:1.00 SG B:CYS120 2.3 9.8 1.0 SG B:CYS134 2.3 11.6 1.0 SG B:CYS137 2.4 9.0 1.0 SG B:CYS117 2.4 9.9 1.0 CB B:CYS117 3.2 10.4 1.0 CB B:CYS137 3.3 9.0 1.0 CB B:CYS120 3.3 9.8 1.0 CB B:CYS134 3.5 10.6 1.0 N B:CYS120 3.8 9.3 1.0 N B:CYS134 4.0 10.1 1.0 CA B:CYS120 4.1 9.4 1.0 CD B:ARG166 4.1 33.5 1.0 N B:CYS137 4.2 8.7 1.0 NH1 B:ARG166 4.2 34.3 1.0 CA B:CYS137 4.3 8.6 1.0 CA B:CYS134 4.3 10.5 1.0 CB B:VAL119 4.4 10.9 1.0 CB B:ASP122 4.7 15.5 1.0 CA B:CYS117 4.7 11.0 1.0 C B:VAL119 4.7 10.2 1.0 C B:CYS120 4.8 10.0 1.0 N B:GLY121 4.9 11.1 1.0 C B:CYS134 4.9 10.4 1.0 NE B:ARG166 4.9 37.2 1.0 CA B:VAL119 5.0 10.4 1.0 O B:CYS134 5.0 9.9 1.0 CZ B:ARG166 5.0 38.6 1.0 N B:ASP122 5.0 12.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Human TR4 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:16.7 occ:1.00 SG B:CYS169 2.2 14.8 1.0 SG B:CYS153 2.3 16.0 1.0 SG B:CYS159 2.3 16.5 1.0 SG B:CYS172 2.4 14.7 1.0 CB B:CYS169 3.2 14.6 1.0 CB B:CYS159 3.2 16.7 1.0 CB B:CYS153 3.3 16.6 1.0 CB B:CYS172 3.4 12.4 1.0 CA B:CYS153 4.0 16.6 1.0 O B:HOH328 4.0 25.5 1.0 N B:CYS159 4.0 18.9 1.0 N B:CYS172 4.2 11.6 1.0 CA B:CYS159 4.2 17.5 1.0 CA B:GLN157 4.3 23.6 1.0 CA B:CYS172 4.4 11.5 1.0 N B:ASP158 4.5 23.8 1.0 N B:GLN157 4.6 21.9 1.0 CA B:CYS169 4.6 16.9 1.0 C B:GLN157 4.8 24.2 1.0 C B:CYS153 4.9 21.9 1.0 O B:HOH362 4.9 38.4 1.0 CD1 B:PHE171 4.9 11.4 1.0 N B:ARG154 4.9 24.1 1.0

Y.Liu, L.Ma, M.Li, Z.Tian, M.Yang, X.Wu, X.Wang, G.Shang, M.Xie, Y.Chen, X.Liu, L.Jiang, W.Wu, C.Xu, L.Xia, G.Li, S.Dai, Z.Chen. Structures of Human TR4LBD-JAZF1 and TR4DBD-Dna Complexes Reveal the Molecular Basis of Transcriptional Regulation Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962