Zinc in PDB 7xv8: Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element

The structure of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element, PDB code: 7xv8 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)	47.71 / 3.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	51.874, 51.874, 241.506, 90, 90, 90
R / Rfree (%)	21.3 / 24.9

The binding sites of Zinc atom in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element (pdb code 7xv8). 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 Homodimer Bound to DR1 Response Element, PDB code: 7xv8:
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 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 Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:61.9 occ:1.00 SG A:CYS120 2.0 53.0 1.0 SG A:CYS134 2.1 56.4 1.0 SG A:CYS137 2.2 58.5 1.0 SG A:CYS117 2.3 67.9 1.0 CB A:CYS117 3.2 63.5 1.0 CB A:CYS120 3.2 50.3 1.0 CB A:CYS137 3.2 63.0 1.0 CB A:CYS134 3.3 55.6 1.0 N A:CYS120 3.8 49.7 1.0 N A:CYS134 3.8 61.9 1.0 CA A:CYS120 4.0 49.0 1.0 NH1 A:ARG166 4.1 55.9 1.0 CA A:CYS134 4.1 55.9 1.0 CB A:VAL119 4.2 53.3 1.0 N A:CYS137 4.2 52.2 1.0 CA A:CYS137 4.3 61.6 1.0 CB A:ASP122 4.6 60.4 1.0 CA A:CYS117 4.7 61.1 1.0 C A:CYS120 4.7 49.1 1.0 C A:VAL119 4.7 58.0 1.0 O A:CYS134 4.8 48.5 1.0 C A:CYS134 4.8 51.7 1.0 N A:GLY121 4.8 46.6 1.0 CA A:VAL119 4.9 62.4 1.0 N A:ASP122 4.9 54.0 1.0 C A:SER133 5.0 63.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain 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 Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:75.3 occ:1.00 SG A:CYS153 2.1 57.2 1.0 SG A:CYS172 2.1 63.1 1.0 SG A:CYS169 2.1 53.2 1.0 SG A:CYS159 2.2 61.8 1.0 CB A:CYS159 3.0 64.8 1.0 CB A:CYS169 3.0 56.2 1.0 CB A:CYS172 3.2 62.4 1.0 CB A:CYS153 3.2 51.7 1.0 N A:CYS159 4.0 73.4 1.0 CA A:CYS159 4.1 68.7 1.0 O A:HOH302 4.1 47.3 1.0 CA A:CYS153 4.2 55.4 1.0 N A:CYS172 4.2 57.7 1.0 CA A:GLN157 4.2 73.5 1.0 CA A:CYS172 4.3 58.4 1.0 CA A:CYS169 4.4 60.1 1.0 C A:GLN157 4.6 77.8 1.0 N A:GLN157 4.7 74.9 1.0 N A:ASP158 4.7 84.1 1.0 CD2 A:PHE171 4.8 65.9 1.0 N A:ARG154 4.9 71.4 1.0 C A:CYS153 4.9 65.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain 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 Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:63.0 occ:1.00 SG B:CYS120 2.0 45.7 1.0 SG B:CYS137 2.1 56.1 1.0 SG B:CYS117 2.3 54.9 1.0 SG B:CYS134 2.4 55.0 1.0 CB B:CYS120 3.0 48.0 1.0 CB B:CYS137 3.4 52.3 1.0 CB B:CYS117 3.4 51.1 1.0 N B:CYS120 3.5 55.8 1.0 CB B:CYS134 3.5 53.5 1.0 CA B:CYS120 3.8 54.3 1.0 N B:CYS134 4.0 63.9 1.0 CB B:VAL119 4.1 52.4 1.0 N B:CYS137 4.3 53.0 1.0 CA B:CYS134 4.3 55.6 1.0 CA B:CYS137 4.4 52.9 1.0 C B:VAL119 4.6 59.9 1.0 N B:GLY121 4.7 60.2 1.0 C B:CYS120 4.7 60.7 1.0 CA B:VAL119 4.8 56.6 1.0 CA B:CYS117 4.8 53.7 1.0 N B:VAL119 4.9 57.0 1.0 CB B:ASP122 4.9 69.7 1.0 NH2 B:ARG173 4.9 56.1 1.0 C B:CYS134 5.0 48.6 1.0 O B:CYS134 5.0 39.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain 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 Homodimer Bound to DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:77.5 occ:1.00 SG B:CYS153 1.8 63.6 1.0 SG B:CYS159 2.1 61.9 1.0 SG B:CYS169 2.2 57.4 1.0 SG B:CYS172 2.3 53.3 1.0 CB B:CYS169 3.0 55.3 1.0 O B:HOH303 3.1 57.9 1.0 CB B:CYS159 3.2 59.8 1.0 CB B:CYS153 3.3 71.6 1.0 CB B:CYS172 3.4 58.4 1.0 CA B:CYS153 4.1 75.4 1.0 N B:CYS172 4.2 59.3 1.0 N B:CYS159 4.2 65.0 1.0 CA B:GLN157 4.2 63.8 1.0 N B:GLN157 4.3 76.4 1.0 CA B:CYS159 4.3 59.9 1.0 CA B:CYS172 4.3 62.4 1.0 CA B:CYS169 4.4 57.2 1.0 CD2 B:PHE171 4.7 77.2 1.0 O B:SER155 4.7 83.8 1.0 N B:ASP158 4.8 58.3 1.0 N B:ARG154 4.8 81.0 1.0 C B:GLN157 4.8 59.6 1.0 N B:SER155 4.9 70.8 1.0 C B:CYS153 4.9 80.7 1.0 C B:SER155 4.9 78.4 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