Zinc in PDB 4cn5: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element, PDB code: 4cn5 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)	43.093 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.286, 44.327, 63.915, 90.00, 98.95, 90.00
R / Rfree (%)	16.73 / 22.7

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element (pdb code 4cn5). 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 Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element, PDB code: 4cn5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 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 NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1210 b:20.7 occ:1.00 SG A:CYS138 2.2 17.4 1.0 SG A:CYS155 2.4 18.4 1.0 SG A:CYS152 2.4 16.8 1.0 SG A:CYS135 2.4 17.9 1.0 CB A:CYS135 3.3 18.9 1.0 CB A:CYS138 3.3 15.4 1.0 CB A:CYS155 3.4 14.7 1.0 CB A:CYS152 3.6 28.3 1.0 N A:CYS138 3.6 15.5 1.0 N A:CYS152 4.0 17.8 1.0 CA A:CYS138 4.0 17.8 1.0 N A:CYS155 4.2 15.1 1.0 CA A:CYS152 4.4 21.7 1.0 CA A:CYS155 4.4 16.3 1.0 NH1 A:ARG184 4.4 18.5 1.0 CB A:ASP140 4.4 17.3 1.0 CB A:ILE137 4.5 21.7 1.0 C A:ILE137 4.6 23.9 1.0 C A:CYS138 4.6 21.5 1.0 N A:GLY139 4.7 16.4 1.0 CA A:CYS135 4.7 18.0 1.0 N A:ASP140 4.8 17.7 1.0 NH2 A:ARG191 4.8 13.5 1.0 CG2 A:ILE137 4.9 15.6 1.0 CD A:ARG184 4.9 19.4 1.0 CA A:ILE137 4.9 20.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 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 NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1211 b:34.4 occ:1.00 SG A:CYS177 2.3 30.9 1.0 SG A:CYS187 2.4 21.9 1.0 SG A:CYS190 2.4 27.4 1.0 SG A:CYS171 2.5 30.0 1.0 CB A:CYS171 3.2 35.2 1.0 CB A:CYS177 3.3 35.7 1.0 CB A:CYS187 3.3 27.0 1.0 CB A:CYS190 3.4 21.9 1.0 N A:CYS177 4.1 31.8 1.0 CL A:CL1214 4.1 57.4 1.0 CA A:CYS171 4.2 33.9 1.0 N A:CYS190 4.2 18.4 1.0 O A:HOH2053 4.3 32.4 1.0 CA A:CYS177 4.3 35.1 1.0 CA A:CYS190 4.4 19.4 1.0 CA A:LYS175 4.4 38.3 1.0 N A:LYS175 4.5 38.1 1.0 N A:ASP176 4.7 48.6 1.0 CA A:CYS187 4.8 18.2 1.0 C A:LYS175 4.8 44.7 1.0 C A:CYS171 4.9 31.7 1.0 N A:ARG172 5.0 30.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 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 NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1210 b:34.1 occ:1.00 SG B:CYS155 2.3 33.7 1.0 SG B:CYS152 2.3 26.4 1.0 SG B:CYS138 2.3 33.8 1.0 SG B:CYS135 2.4 31.7 1.0 CB B:CYS155 3.2 26.3 1.0 CB B:CYS135 3.3 31.8 1.0 CB B:CYS138 3.4 35.0 1.0 CB B:CYS152 3.6 28.2 1.0 N B:CYS152 3.9 25.4 1.0 N B:CYS138 3.9 36.4 1.0 N B:CYS155 4.1 22.6 1.0 CA B:CYS138 4.2 40.7 1.0 CA B:CYS155 4.3 23.9 1.0 CA B:CYS152 4.3 25.1 1.0 NH1 B:ARG184 4.3 34.1 1.0 CB B:ILE137 4.5 38.6 1.0 CB B:ASP140 4.5 42.1 1.0 NH2 B:ARG191 4.6 26.0 1.0 CA B:CYS135 4.8 33.5 1.0 N B:GLY139 4.8 39.0 1.0 C B:CYS138 4.8 39.3 1.0 C B:CYS152 4.9 30.1 1.0 O B:CYS152 4.9 21.5 1.0 C B:ILE137 4.9 41.7 1.0 N B:ASP140 4.9 38.1 1.0 CG2 B:ILE137 4.9 35.9 1.0 CD B:ARG184 5.0 33.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 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 NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1211 b:63.0 occ:1.00 SG B:CYS187 2.3 50.6 1.0 SG B:CYS190 2.4 54.8 1.0 SG B:CYS177 2.4 63.6 1.0 SG B:CYS171 2.5 62.7 1.0 CB B:CYS177 3.3 57.0 1.0 CB B:CYS190 3.3 49.4 1.0 CB B:CYS171 3.4 65.1 1.0 CB B:CYS187 3.4 58.3 1.0 N B:CYS177 3.7 68.1 1.0 CA B:CYS177 4.1 66.4 1.0 N B:CYS190 4.1 46.0 1.0 CA B:CYS171 4.2 60.7 1.0 CA B:CYS190 4.3 48.5 1.0 N B:ASP176 4.5 72.6 1.0 O B:HOH2042 4.7 46.8 1.0 CD2 B:TYR189 4.7 59.0 1.0 C B:LYS175 4.7 68.5 1.0 CA B:LYS175 4.7 75.0 1.0 C B:ASP176 4.8 72.6 1.0 C B:CYS171 4.8 62.5 1.0 CA B:CYS187 4.8 44.8 1.0 CA B:ASP176 4.9 76.0 1.0 CB B:TYR189 5.0 49.2 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