Zinc in PDB 2nll: Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna

The structure of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna, PDB code: 2nll was solved by F.Rastinejad, T.Perlmann, R.M.Evans, P.B.Sigler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.900, 65.600, 125.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.9

The structure of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Zinc atom in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna (pdb code 2nll). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna, PDB code: 2nll:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn250 b:56.4 occ:1.00 SG A:CYS152 2.3 57.6 1.0 SG A:CYS155 2.3 51.4 1.0 SG A:CYS138 2.3 59.0 1.0 SG A:CYS135 2.4 55.4 1.0 CB A:CYS135 3.2 54.4 1.0 CB A:CYS152 3.3 59.5 1.0 CB A:CYS138 3.4 54.4 1.0 CB A:CYS155 3.4 46.8 1.0 N A:CYS138 3.6 52.2 1.0 N A:CYS155 4.0 43.7 1.0 N A:CYS152 4.0 55.0 1.0 CA A:CYS138 4.1 53.3 1.0 CA A:CYS152 4.2 56.8 1.0 CA A:CYS155 4.3 45.0 1.0 CB A:ILE137 4.4 56.6 1.0 NH1 A:ARG184 4.4 50.4 1.0 NH2 A:ARG191 4.5 32.5 1.0 CB A:ASP140 4.6 58.0 1.0 CA A:CYS135 4.7 53.4 1.0 O A:ASP140 4.7 59.2 1.0 C A:CYS138 4.7 55.1 1.0 C A:ILE137 4.7 53.0 1.0 C A:CYS152 4.9 56.6 1.0 N A:ASP140 4.9 58.1 1.0 O A:CYS152 4.9 55.9 1.0 CA A:ILE137 5.0 54.9 1.0

Zinc binding site 2 out of 4 in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn251 b:44.6 occ:1.00 SG A:CYS187 2.3 41.0 1.0 SG A:CYS190 2.3 45.4 1.0 SG A:CYS171 2.3 42.7 1.0 SG A:CYS177 2.3 47.6 1.0 CB A:CYS171 3.3 44.6 1.0 CB A:CYS187 3.3 35.1 1.0 CB A:CYS177 3.4 49.4 1.0 CB A:CYS190 3.5 44.7 1.0 CA A:CYS171 4.0 49.6 1.0 N A:CYS190 4.0 46.9 1.0 O A:HOH636 4.1 18.7 1.0 CA A:LYS175 4.3 53.9 1.0 N A:LYS175 4.3 54.7 1.0 CA A:CYS190 4.3 45.8 1.0 N A:CYS177 4.4 53.9 1.0 CB A:TYR189 4.5 49.2 1.0 CA A:CYS177 4.6 51.9 1.0 OD1 A:ASP176 4.7 55.6 1.0 CD1 A:TYR189 4.7 50.1 1.0 CA A:CYS187 4.7 35.7 1.0 N A:ASP176 4.7 56.8 1.0 N A:ARG172 4.7 47.5 1.0 OD2 A:ASP173 4.8 52.4 1.0 C A:CYS171 4.8 49.2 1.0 N A:ASP173 4.9 49.3 1.0

Zinc binding site 3 out of 4 in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:17.5 occ:1.00 SG B:CYS303 2.3 14.2 1.0 SG B:CYS323 2.3 16.6 1.0 SG B:CYS306 2.4 18.2 1.0 SG B:CYS320 2.4 14.9 1.0 CB B:CYS303 3.3 15.2 1.0 CB B:CYS323 3.4 14.8 1.0 CB B:CYS306 3.5 17.9 1.0 CB B:CYS320 3.6 8.8 1.0 N B:CYS306 3.7 12.2 1.0 N B:CYS323 4.1 17.3 1.0 N B:CYS320 4.1 15.1 1.0 CA B:CYS306 4.1 14.0 1.0 NH1 B:ARG354 4.2 15.1 1.0 CA B:CYS323 4.3 17.4 1.0 CA B:CYS320 4.4 16.9 1.0 CB B:VAL305 4.5 14.1 1.0 CB B:ASP308 4.6 19.1 1.0 CA B:CYS303 4.7 18.7 1.0 C B:VAL305 4.7 10.6 1.0 NH2 B:ARG361 4.8 10.5 1.0 C B:CYS306 4.8 15.3 1.0 N B:GLY307 4.8 17.1 1.0 CD B:ARG354 4.8 13.8 1.0 O B:CYS320 4.8 16.0 1.0 N B:ASP308 4.9 21.3 1.0 C B:CYS320 5.0 19.2 1.0

Zinc binding site 4 out of 4 in the Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound to Thyroid Response Element Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn451 b:23.8 occ:1.00 SG B:CYS360 2.3 20.9 1.0 SG B:CYS347 2.3 25.5 1.0 SG B:CYS341 2.3 23.2 1.0 SG B:CYS357 2.3 16.4 1.0 CB B:CYS357 3.3 21.0 1.0 CB B:CYS341 3.3 29.9 1.0 CB B:CYS347 3.3 24.1 1.0 CB B:CYS360 3.4 16.9 1.0 CA B:CYS341 4.0 33.6 1.0 O B:HOH691 4.1 37.1 1.0 N B:CYS347 4.2 21.2 1.0 N B:CYS360 4.3 21.9 1.0 O B:GLU344 4.3 43.9 1.0 CA B:CYS347 4.4 22.4 1.0 CA B:CYS360 4.4 17.8 1.0 CA B:GLY345 4.4 30.8 1.0 CA B:CYS357 4.7 22.1 1.0 O B:HOH646 4.7 53.6 1.0 C B:CYS341 4.8 35.9 1.0 N B:LYS342 4.8 42.3 1.0 N B:LYS346 4.8 24.4 1.0 C B:GLY345 4.9 27.9 1.0

F.Rastinejad, T.Perlmann, R.M.Evans, P.B.Sigler. Structural Determinants of Nuclear Receptor Assembly on Dna Direct Repeats. Nature V. 375 203 1995.
ISSN: ISSN 0028-0836
PubMed: 7746322
DOI: 10.1038/375203A0