Zinc in PDB 4cn3: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element, PDB code: 4cn3 was solved by A.G.Mcewen, P.Poussin-Courmontagne, J.Osz, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.57 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.910, 69.280, 138.860, 90.00, 90.00, 90.00
R / Rfree (%)	17.94 / 24.93

The binding sites of Zinc atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element (pdb code 4cn3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element, PDB code: 4cn3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA 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 Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1209 b:20.4 occ:1.00 SG A:CYS155 2.2 21.5 1.0 SG A:CYS152 2.3 21.9 1.0 SG A:CYS138 2.3 19.1 1.0 SG A:CYS135 2.4 23.7 1.0 CB A:CYS155 3.2 17.0 1.0 CB A:CYS135 3.4 20.8 1.0 CB A:CYS138 3.5 15.9 1.0 CB A:CYS152 3.6 18.6 1.0 N A:CYS138 3.8 15.6 1.0 N A:CYS152 3.9 19.4 1.0 N A:CYS155 4.0 16.5 1.0 CA A:CYS155 4.2 16.5 1.0 CA A:CYS138 4.2 16.7 1.0 CA A:CYS152 4.3 18.5 1.0 NH1 A:ARG184 4.5 19.6 1.0 CB A:ILE137 4.5 18.8 1.0 CB A:ASP140 4.5 20.6 1.0 NH2 A:ARG191 4.7 25.8 1.0 CA A:CYS135 4.8 21.8 1.0 C A:ILE137 4.8 21.1 1.0 CG2 A:ILE137 4.9 18.8 1.0 CD A:ARG184 4.9 21.7 1.0 C A:CYS138 4.9 22.4 1.0 N A:ASP140 4.9 20.8 1.0 C A:CYS152 5.0 20.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA 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 Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1210 b:30.6 occ:1.00 SG A:CYS177 2.3 31.3 1.0 SG A:CYS187 2.3 24.2 1.0 SG A:CYS171 2.4 25.7 1.0 SG A:CYS190 2.4 26.6 1.0 CB A:CYS177 3.2 28.1 1.0 CB A:CYS171 3.3 21.8 1.0 CB A:CYS187 3.3 20.6 1.0 CB A:CYS190 3.5 22.3 1.0 CA A:CYS171 4.0 22.0 1.0 O A:HOH2038 4.1 33.7 1.0 N A:CYS177 4.1 32.1 1.0 N A:CYS190 4.3 21.5 1.0 CA A:CYS177 4.3 30.3 1.0 CA A:LYS175 4.4 31.0 1.0 N A:LYS175 4.5 31.9 1.0 CA A:CYS190 4.5 22.1 1.0 N A:ASP176 4.7 35.1 1.0 CA A:CYS187 4.7 19.6 1.0 CB A:ASP173 4.8 33.8 1.0 C A:CYS171 4.9 31.1 1.0 N A:ARG172 4.9 30.0 1.0 N A:ASP173 4.9 31.3 1.0 CB A:TYR189 4.9 21.9 1.0 C A:LYS175 4.9 36.7 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA 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 Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1209 b:27.3 occ:1.00 SG B:CYS152 2.2 23.6 1.0 SG B:CYS135 2.3 28.3 1.0 SG B:CYS138 2.3 23.2 1.0 SG B:CYS155 2.6 22.6 1.0 CB B:CYS135 3.3 25.2 1.0 CB B:CYS138 3.4 19.5 1.0 CB B:CYS155 3.5 18.1 1.0 CB B:CYS152 3.5 20.7 1.0 N B:CYS138 3.7 21.3 1.0 N B:CYS152 3.9 20.0 1.0 CA B:CYS138 4.0 20.9 1.0 N B:CYS155 4.2 17.5 1.0 CA B:CYS152 4.3 19.8 1.0 CB B:ILE137 4.4 21.8 1.0 CA B:CYS155 4.5 17.7 1.0 NH1 B:ARG184 4.5 20.3 1.0 CB B:ASP140 4.5 25.6 1.0 C B:ILE137 4.6 24.7 1.0 CA B:CYS135 4.8 25.9 1.0 C B:CYS138 4.8 23.1 1.0 CD B:ARG184 4.9 35.2 1.0 NH2 B:ARG191 4.9 21.6 1.0 CA B:ILE137 4.9 20.3 1.0 CG1 B:ILE137 5.0 20.8 1.0 N B:GLY139 5.0 21.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA 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 Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1210 b:34.6 occ:1.00 SG B:CYS171 2.3 39.3 1.0 SG B:CYS187 2.4 32.2 1.0 SG B:CYS190 2.4 31.1 1.0 SG B:CYS177 2.4 30.4 1.0 CB B:CYS187 3.2 28.0 1.0 CB B:CYS171 3.3 35.6 1.0 CB B:CYS177 3.3 25.1 1.0 CB B:CYS190 3.5 24.6 1.0 CA B:CYS171 4.0 35.1 1.0 N B:CYS177 4.1 26.5 1.0 N B:CYS190 4.2 21.9 1.0 CA B:CYS177 4.4 25.8 1.0 CA B:CYS190 4.4 22.6 1.0 N B:LYS175 4.4 31.3 1.0 CA B:LYS175 4.4 29.3 1.0 N B:ARG172 4.5 39.5 1.0 N B:ASP176 4.7 26.9 1.0 CA B:CYS187 4.7 27.6 1.0 C B:CYS171 4.7 42.6 1.0 CD2 B:TYR189 4.7 26.5 1.0 N B:ASP173 4.8 38.5 1.0 C B:LYS175 4.8 30.0 1.0 O B:HOH2017 4.8 43.6 1.0 CB B:TYR189 4.9 23.3 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1210 b:22.4 occ:1.00 SG C:CYS135 2.2 20.7 1.0 SG C:CYS138 2.3 20.9 1.0 SG C:CYS152 2.4 20.3 1.0 SG C:CYS155 2.5 17.8 1.0 CB C:CYS135 3.2 17.1 1.0 CB C:CYS155 3.4 13.5 1.0 CB C:CYS138 3.4 17.2 1.0 CB C:CYS152 3.5 16.8 1.0 N C:CYS138 3.8 16.6 1.0 NH1 C:ARG184 4.0 21.5 1.0 N C:CYS152 4.0 16.3 1.0 CA C:CYS138 4.1 17.3 1.0 N C:CYS155 4.2 13.1 1.0 CA C:CYS152 4.4 16.3 1.0 CA C:CYS155 4.4 13.7 1.0 CB C:ILE137 4.4 18.0 1.0 CB C:ASP140 4.5 20.7 1.0 CA C:CYS135 4.7 18.0 1.0 C C:ILE137 4.7 20.2 1.0 C C:CYS138 4.8 21.3 1.0 CG1 C:ILE137 4.9 17.8 1.0 CD C:ARG184 4.9 16.2 1.0 CA C:ILE137 5.0 16.2 1.0 NH2 C:ARG191 5.0 10.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1211 b:29.8 occ:1.00 SG C:CYS171 2.2 27.5 1.0 SG C:CYS187 2.3 22.6 1.0 SG C:CYS190 2.3 24.0 1.0 SG C:CYS177 2.5 29.2 1.0 CB C:CYS171 3.2 24.2 1.0 CB C:CYS177 3.3 23.3 1.0 CB C:CYS187 3.3 19.1 1.0 CB C:CYS190 3.3 19.1 1.0 CA C:CYS171 3.9 25.3 1.0 N C:CYS177 4.1 22.0 1.0 N C:CYS190 4.2 19.7 1.0 O C:HOH2032 4.3 27.5 1.0 CA C:CYS177 4.3 22.0 1.0 CA C:CYS190 4.3 18.4 1.0 CA C:LYS175 4.4 29.3 1.0 N C:LYS175 4.4 30.6 1.0 N C:ASP176 4.7 31.2 1.0 CA C:CYS187 4.7 19.7 1.0 C C:LYS175 4.8 35.1 1.0 C C:CYS171 4.8 31.1 1.0 CD2 C:TYR189 4.9 21.9 1.0 N C:ARG172 4.9 30.0 1.0 CB C:TYR189 4.9 20.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1210 b:20.6 occ:1.00 SG D:CYS138 2.2 23.6 1.0 SG D:CYS155 2.2 16.1 1.0 SG D:CYS152 2.3 23.4 1.0 SG D:CYS135 2.5 22.9 1.0 CB D:CYS138 3.4 19.9 1.0 CB D:CYS155 3.4 12.9 1.0 CB D:CYS135 3.4 20.3 1.0 CB D:CYS152 3.6 20.2 1.0 N D:CYS138 3.7 19.1 1.0 N D:CYS152 3.9 18.5 1.0 CA D:CYS138 4.0 20.0 1.0 NH1 D:ARG184 4.0 27.9 1.0 N D:CYS155 4.2 14.6 1.0 CA D:CYS152 4.3 19.3 1.0 CA D:CYS155 4.4 13.8 1.0 CB D:ILE137 4.4 20.9 1.0 CB D:ASP140 4.6 20.2 1.0 C D:ILE137 4.6 22.4 1.0 C D:CYS138 4.8 26.5 1.0 CA D:CYS135 4.8 21.3 1.0 CD D:ARG184 4.8 12.3 1.0 NH2 D:ARG191 4.8 13.2 1.0 N D:GLY139 4.8 22.9 1.0 CD1 D:ILE137 4.9 19.4 1.0 CA D:ILE137 4.9 18.6 1.0 CG2 D:ILE137 4.9 20.5 1.0 O D:CYS152 4.9 24.0 1.0 N D:ASP140 4.9 20.8 1.0 C D:CYS152 5.0 24.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human GDE1SPA Response Element within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1211 b:28.4 occ:1.00 SG D:CYS187 2.3 27.2 1.0 SG D:CYS171 2.3 26.4 1.0 SG D:CYS177 2.4 33.6 1.0 SG D:CYS190 2.5 27.8 1.0 CB D:CYS177 3.1 28.3 1.0 CB D:CYS187 3.4 22.7 1.0 CB D:CYS171 3.4 23.1 1.0 CB D:CYS190 3.5 22.6 1.0 O D:HOH2033 4.0 39.9 1.0 N D:CYS190 4.1 20.7 1.0 CA D:CYS171 4.2 25.0 1.0 N D:CYS177 4.2 29.4 1.0 O D:HOH2036 4.2 30.5 1.0 CA D:CYS177 4.3 28.9 1.0 CA D:CYS190 4.4 21.4 1.0 CA D:LYS175 4.4 28.6 1.0 N D:LYS175 4.5 30.0 1.0 CA D:CYS187 4.8 21.8 1.0 CB D:TYR189 4.9 21.1 1.0 C D:LYS175 4.9 35.8 1.0 N D:ASP176 4.9 32.3 1.0 CB D:ASP173 5.0 35.2 1.0 C D:CYS171 5.0 33.2 1.0

J.Osz, A.G.Mcewen, P.Poussin-Courmontagne, E.Moutier, C.Birck, I.Davidson, D.Moras, N.Rochel. Structural Basis of Natural Promoter Recognition By the Retinoid X Nuclear Receptor. Sci.Rep. V. 5 8216 2015.
ISSN: ISSN 2045-2322
PubMed: 25645674
DOI: 10.1038/SREP08216