Zinc in PDB 7xv6: Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element

The structure of Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element, PDB code: 7xv6 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)	31.53 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.146, 52.146, 242.701, 90, 90, 90
R / Rfree (%)	18.8 / 21.5

The binding sites of Zinc atom in the Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element (pdb code 7xv6). 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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element, PDB code: 7xv6:
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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element


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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:28.6 occ:1.00 SG A:CYS137 2.2 24.7 1.0 SG A:CYS120 2.2 24.3 1.0 SG A:CYS134 2.3 26.5 1.0 SG A:CYS117 2.3 28.3 1.0 CB A:CYS117 3.1 27.4 1.0 CB A:CYS137 3.3 21.7 1.0 CB A:CYS120 3.4 28.2 1.0 CB A:CYS134 3.5 25.9 1.0 N A:CYS120 3.7 28.3 1.0 N A:CYS134 3.9 25.4 1.0 N A:CYS137 4.1 21.9 1.0 CA A:CYS120 4.2 27.1 1.0 CA A:CYS134 4.3 25.2 1.0 CA A:CYS137 4.3 20.3 1.0 NH1 A:ARG166 4.3 43.4 1.0 CB A:VAL119 4.4 30.2 1.0 CA A:CYS117 4.6 28.7 1.0 CB A:ASP122 4.7 43.7 1.0 NH2 A:ARG173 4.7 34.9 1.0 C A:VAL119 4.7 31.0 1.0 C A:CYS120 4.8 30.1 1.0 N A:GLY121 4.8 32.5 1.0 CG1 A:VAL119 4.9 30.4 1.0 O A:CYS134 4.9 22.8 1.0 C A:CYS134 4.9 24.6 1.0 CA A:VAL119 4.9 29.5 1.0 N A:VAL119 5.0 30.7 1.0 N A:ASP122 5.0 35.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element


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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:29.3 occ:1.00 SG A:CYS159 2.3 26.4 1.0 SG A:CYS153 2.3 27.6 1.0 SG A:CYS172 2.4 24.1 1.0 SG A:CYS169 2.4 22.6 1.0 CB A:CYS159 3.1 25.9 1.0 CB A:CYS169 3.3 23.9 1.0 CB A:CYS172 3.4 23.6 1.0 CB A:CYS153 3.4 26.3 1.0 N A:CYS159 3.9 29.1 1.0 O A:HOH306 4.0 41.1 1.0 CA A:CYS159 4.1 27.8 1.0 CA A:GLN157 4.1 34.1 1.0 N A:CYS172 4.1 23.6 1.0 CA A:CYS153 4.1 27.0 1.0 O A:HOH301 4.2 34.9 1.0 N A:GLN157 4.3 36.4 1.0 CA A:CYS172 4.3 24.6 1.0 N A:ASP158 4.4 28.8 1.0 O A:HOH335 4.5 29.9 1.0 OG A:SER155 4.6 46.9 1.0 C A:GLN157 4.6 29.8 1.0 CA A:CYS169 4.7 25.3 1.0 O A:SER155 4.8 48.3 0.7 CD1 A:PHE171 4.8 29.9 1.0 N A:ARG154 5.0 34.5 1.0 C A:CYS153 5.0 31.1 1.0 C A:ASP158 5.0 29.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element


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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:24.7 occ:1.00 SG B:CYS117 2.3 24.4 1.0 SG B:CYS120 2.3 24.4 1.0 SG B:CYS137 2.3 24.3 1.0 SG B:CYS134 2.3 23.6 1.0 CB B:CYS117 3.2 26.8 1.0 CB B:CYS120 3.3 23.8 1.0 CB B:CYS137 3.4 26.0 1.0 N B:CYS120 3.6 24.7 1.0 CB B:CYS134 3.6 23.4 1.0 N B:CYS134 3.9 26.0 1.0 CA B:CYS120 4.0 26.9 1.0 N B:CYS137 4.0 23.9 1.0 NH1 B:ARG166 4.2 25.8 1.0 CA B:CYS134 4.3 24.5 1.0 CA B:CYS137 4.3 27.3 1.0 CB B:VAL119 4.3 29.4 1.0 C B:VAL119 4.6 26.2 1.0 CA B:CYS117 4.7 25.3 1.0 CG1 B:VAL119 4.7 28.1 1.0 C B:CYS120 4.7 26.4 1.0 CB B:ASP122 4.7 29.9 1.0 N B:GLY121 4.8 25.0 1.0 NH2 B:ARG173 4.8 20.6 1.0 O B:CYS134 4.8 19.3 1.0 CA B:VAL119 4.9 28.1 1.0 C B:CYS134 4.9 22.5 1.0 CD B:ARG166 5.0 23.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element


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 with C-Terminal Extension (Dbd-Cte) Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:24.9 occ:1.00 SG B:CYS172 2.1 26.6 1.0 SG B:CYS169 2.2 19.4 1.0 SG B:CYS159 2.4 27.4 1.0 SG B:CYS153 2.4 27.9 1.0 CB B:CYS169 3.1 22.4 1.0 CB B:CYS159 3.1 28.6 1.0 CB B:CYS172 3.2 26.2 1.0 CB B:CYS153 3.3 25.9 1.0 N B:CYS172 4.1 21.2 1.0 N B:CYS159 4.1 29.5 1.0 CA B:CYS153 4.1 27.0 1.0 CA B:GLN157 4.2 40.7 1.0 CA B:CYS172 4.2 25.2 1.0 CA B:CYS159 4.2 30.1 1.0 N B:GLN157 4.3 37.4 1.0 O B:SER155 4.5 73.4 1.0 O B:HOH329 4.5 31.9 1.0 CA B:CYS169 4.6 23.9 1.0 N B:ASP158 4.7 37.6 1.0 C B:GLN157 4.8 36.1 1.0 CD1 B:PHE171 4.9 25.6 1.0 C B:CYS153 4.9 32.0 1.0 CG A:PRO193 4.9 31.4 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