Zinc in PDB 4cn7: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element, PDB code: 4cn7 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)	40.82 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.630, 65.350, 209.120, 90.00, 90.00, 90.00
R / Rfree (%)	17.31 / 20.93

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element (pdb code 4cn7). 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 An Idealized DR1 Response Element, PDB code: 4cn7:
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 An Idealized 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 Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1205 b:50.8 occ:1.00 SG A:CYS135 2.2 46.4 1.0 SG A:CYS138 2.3 46.8 1.0 SG A:CYS155 2.4 52.8 1.0 SG A:CYS152 2.5 49.5 1.0 CB A:CYS135 3.2 44.2 1.0 CB A:CYS138 3.3 43.0 1.0 CB A:CYS155 3.4 47.9 1.0 N A:CYS138 3.6 42.6 1.0 CB A:CYS152 3.6 46.5 1.0 CA A:CYS138 4.0 43.5 1.0 N A:CYS152 4.0 44.4 1.0 N A:CYS155 4.3 49.0 1.0 NH1 A:ARG184 4.3 47.9 1.0 CA A:CYS152 4.4 45.5 1.0 CA A:CYS155 4.4 47.7 1.0 CB A:ILE137 4.5 43.7 1.0 CB A:ASP140 4.6 52.1 1.0 C A:ILE137 4.6 46.8 1.0 CA A:CYS135 4.6 45.6 1.0 C A:CYS138 4.7 51.0 1.0 N A:GLY139 4.8 47.5 1.0 N A:ASP140 4.9 48.6 1.0 CD A:ARG184 4.9 55.6 1.0 CA A:ILE137 4.9 42.8 1.0 CG2 A:ILE137 4.9 41.0 1.0 NH2 A:ARG191 5.0 51.1 1.0 O A:CYS152 5.0 52.7 1.0 N A:ILE137 5.0 45.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized 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 Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1206 b:69.3 occ:1.00 SG A:CYS187 2.3 65.2 1.0 SG A:CYS171 2.3 80.4 1.0 SG A:CYS177 2.3 72.6 1.0 SG A:CYS190 2.4 67.7 1.0 CB A:CYS187 3.1 60.6 1.0 CB A:CYS177 3.2 65.4 1.0 CB A:CYS190 3.4 59.9 1.0 CB A:CYS171 3.4 77.0 1.0 CA A:CYS171 4.1 77.8 1.0 N A:CYS177 4.1 68.1 1.0 N A:CYS190 4.2 60.3 1.0 CA A:CYS177 4.3 66.8 1.0 O A:HOH2021 4.3 58.6 1.0 CA A:CYS190 4.4 58.6 1.0 CA A:LYS175 4.5 70.3 1.0 CA A:CYS187 4.6 59.5 1.0 N A:LYS175 4.7 73.8 1.0 N A:ASP176 4.8 71.9 1.0 C A:CYS171 4.9 83.5 1.0 N A:ARG172 4.9 79.1 1.0 NE2 B:GLN210 4.9 0.6 1.0 CD2 A:TYR189 4.9 67.9 1.0 C A:LYS175 4.9 73.9 1.0 N A:ASP173 5.0 81.6 1.0 CB A:TYR189 5.0 64.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized 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 Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1211 b:54.4 occ:1.00 SG B:CYS138 2.3 59.7 1.0 SG B:CYS155 2.3 48.9 1.0 SG B:CYS152 2.3 47.9 1.0 SG B:CYS135 2.4 52.5 1.0 CB B:CYS155 3.3 43.6 1.0 CB B:CYS135 3.3 51.6 1.0 CB B:CYS138 3.4 55.6 1.0 CB B:CYS152 3.5 46.6 1.0 N B:CYS138 3.6 54.1 1.0 N B:CYS152 4.0 45.3 1.0 CA B:CYS138 4.0 55.7 1.0 N B:CYS155 4.1 43.4 1.0 NH1 B:ARG184 4.3 61.6 1.0 CA B:CYS155 4.3 42.9 1.0 CA B:CYS152 4.3 45.9 1.0 CB B:ILE137 4.5 52.3 1.0 C B:ILE137 4.6 57.0 1.0 CB B:ASP140 4.7 59.5 1.0 N B:GLY139 4.7 56.8 1.0 C B:CYS138 4.8 60.5 1.0 CA B:CYS135 4.8 54.2 1.0 CD B:ARG184 4.8 63.1 1.0 NH2 B:ARG191 4.8 42.1 1.0 N B:ASP140 4.9 58.6 1.0 CG2 B:ILE137 4.9 54.1 1.0 CA B:ILE137 4.9 51.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized 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 Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1212 b:70.0 occ:1.00 SG B:CYS171 2.2 77.6 1.0 SG B:CYS190 2.3 59.4 1.0 SG B:CYS187 2.3 61.2 1.0 SG B:CYS177 2.5 71.9 1.0 CB B:CYS171 3.2 73.2 1.0 CB B:CYS187 3.3 56.8 1.0 CB B:CYS177 3.4 66.0 1.0 CB B:CYS190 3.4 51.5 1.0 CA B:CYS171 4.0 72.9 1.0 N B:CYS177 4.1 69.1 1.0 N B:CYS190 4.2 50.0 1.0 CA B:LYS175 4.3 77.1 1.0 O B:HOH2022 4.3 54.5 1.0 CA B:CYS177 4.4 67.7 1.0 CA B:CYS190 4.4 49.2 1.0 N B:LYS175 4.5 82.2 1.0 N B:ASP176 4.6 74.3 1.0 O B:HOH2023 4.7 39.9 1.0 C B:LYS175 4.7 79.5 1.0 CD2 B:TYR189 4.7 60.2 1.0 CA B:CYS187 4.8 55.8 1.0 C B:CYS171 4.8 82.8 1.0 CB B:TYR189 4.9 53.1 1.0 N B:ARG172 4.9 81.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 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 An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1208 b:63.8 occ:1.00 SG E:CYS155 2.3 63.0 1.0 SG E:CYS152 2.3 60.1 1.0 SG E:CYS138 2.3 70.1 1.0 SG E:CYS135 2.4 71.3 1.0 CB E:CYS155 3.2 55.4 1.0 CB E:CYS138 3.4 67.0 1.0 CB E:CYS135 3.5 71.3 1.0 CB E:CYS152 3.7 59.5 1.0 N E:CYS138 3.7 66.2 1.0 N E:CYS152 4.0 59.1 1.0 N E:CYS155 4.0 53.4 1.0 CA E:CYS138 4.1 68.3 1.0 CA E:CYS155 4.2 52.4 1.0 NH1 E:ARG184 4.3 77.6 1.0 CA E:CYS152 4.4 59.1 1.0 CB E:ILE137 4.5 63.3 1.0 CB E:ASP140 4.6 73.3 1.0 N E:GLY139 4.7 72.1 1.0 C E:ILE137 4.7 69.9 1.0 NH2 E:ARG191 4.7 57.8 1.0 CD E:ARG184 4.8 53.1 1.0 C E:CYS138 4.8 74.3 1.0 N E:ASP140 4.9 73.7 1.0 CA E:CYS135 4.9 73.9 1.0 CG2 E:ILE137 4.9 63.3 1.0 O E:CYS152 4.9 58.8 1.0 C E:CYS152 5.0 61.0 1.0 CA E:ILE137 5.0 64.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 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 An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1209 b:90.0 occ:1.00 SG E:CYS171 2.2 87.8 1.0 SG E:CYS190 2.3 82.7 1.0 SG E:CYS187 2.3 78.3 1.0 SG E:CYS177 2.5 94.5 1.0 CB E:CYS187 3.3 73.1 1.0 CB E:CYS171 3.3 83.0 1.0 CB E:CYS177 3.3 87.6 1.0 CB E:CYS190 3.4 73.0 1.0 CA E:CYS171 4.0 82.8 1.0 N E:CYS190 4.1 67.7 1.0 N E:CYS177 4.2 92.1 1.0 CA E:CYS177 4.4 90.4 1.0 CA E:CYS190 4.4 69.0 1.0 CA E:LYS175 4.4 91.6 1.0 N E:LYS175 4.6 96.1 1.0 N E:ASP176 4.7 95.6 1.0 CA E:CYS187 4.7 69.7 1.0 C E:CYS171 4.8 90.0 1.0 C E:LYS175 4.8 96.0 1.0 CD1 E:TYR189 4.8 77.7 1.0 N E:ARG172 4.9 87.2 1.0 CB E:TYR189 4.9 70.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 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 An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1211 b:49.8 occ:1.00 SG F:CYS138 2.3 48.7 1.0 SG F:CYS135 2.3 53.0 1.0 SG F:CYS152 2.3 52.0 1.0 SG F:CYS155 2.4 47.1 1.0 CB F:CYS135 3.3 51.5 1.0 CB F:CYS155 3.3 43.3 1.0 CB F:CYS138 3.4 46.5 1.0 CB F:CYS152 3.6 49.2 1.0 N F:CYS138 3.8 48.6 1.0 N F:CYS152 4.0 47.6 1.0 CA F:CYS138 4.1 48.9 1.0 N F:CYS155 4.2 45.1 1.0 NH1 F:ARG184 4.3 41.8 1.0 CA F:CYS155 4.3 43.4 1.0 CA F:CYS152 4.4 47.6 1.0 CB F:ILE137 4.5 49.7 1.0 CB F:ASP140 4.6 59.4 1.0 C F:ILE137 4.7 53.2 1.0 CA F:CYS135 4.7 54.0 1.0 CD F:ARG184 4.8 50.2 1.0 C F:CYS138 4.9 56.9 1.0 CG2 F:ILE137 4.9 48.8 1.0 NH2 F:ARG191 4.9 35.4 1.0 O F:CYS152 4.9 45.6 1.0 CA F:ILE137 4.9 50.0 1.0 C F:CYS152 5.0 48.2 1.0 N F:ASP140 5.0 60.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to An Idealized DR1 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 An Idealized DR1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1212 b:62.0 occ:1.00 SG F:CYS171 2.2 68.6 1.0 SG F:CYS187 2.3 56.6 1.0 SG F:CYS177 2.4 69.2 1.0 SG F:CYS190 2.4 60.4 1.0 CB F:CYS187 3.2 50.8 1.0 CB F:CYS177 3.3 63.7 1.0 CB F:CYS171 3.4 65.0 1.0 CB F:CYS190 3.5 53.3 1.0 O F:HOH2016 3.9 72.6 1.0 CA F:CYS171 4.1 64.8 1.0 N F:CYS177 4.1 65.6 1.0 CA F:CYS177 4.3 65.3 1.0 N F:CYS190 4.3 52.0 1.0 CA F:LYS175 4.5 63.8 1.0 CA F:CYS190 4.5 52.3 1.0 N F:LYS175 4.6 66.1 1.0 CA F:CYS187 4.7 49.6 1.0 N F:ASP176 4.7 68.4 1.0 O F:HOH2017 4.7 72.1 1.0 N F:ARG172 4.8 68.0 1.0 C F:CYS171 4.8 70.9 1.0 C F:LYS175 4.9 68.9 1.0 CB F:ASP173 4.9 76.6 1.0 N F:ASP173 4.9 74.6 1.0 CD1 F:TYR189 5.0 61.5 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