Zinc in PDB 4cn2: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element, PDB code: 4cn2 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)	23.898 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.234, 43.952, 63.316, 90.00, 106.02, 90.00
R / Rfree (%)	16.48 / 21.42

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element (pdb code 4cn2). 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 RAMP2 Response Element, PDB code: 4cn2:
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 RAMP2 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 RAMP2 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1211 b:26.9 occ:1.00 SG C:CYS152 2.3 17.2 1.0 SG C:CYS138 2.3 16.4 1.0 SG C:CYS135 2.4 17.3 1.0 SG C:CYS155 2.4 15.7 1.0 CB C:CYS135 3.2 20.2 1.0 CB C:CYS155 3.3 11.8 1.0 CB C:CYS138 3.4 12.9 1.0 CB C:CYS152 3.5 14.7 1.0 N C:CYS138 3.7 15.1 1.0 N C:CYS152 3.9 10.9 1.0 N C:CYS155 4.1 13.7 1.0 CA C:CYS138 4.1 19.0 1.0 NH1 C:ARG184 4.3 20.4 1.0 CA C:CYS152 4.3 10.6 1.0 CA C:CYS155 4.3 13.6 1.0 CB C:ILE137 4.4 21.1 1.0 CB C:ASP140 4.4 20.9 1.0 C C:ILE137 4.7 20.6 1.0 CA C:CYS135 4.7 15.9 1.0 C C:CYS138 4.7 19.2 1.0 CG2 C:ILE137 4.8 18.9 1.0 N C:GLY139 4.8 16.8 1.0 N C:ASP140 4.8 16.4 1.0 NH2 C:ARG191 4.9 13.7 1.0 CA C:ILE137 4.9 15.6 1.0 C C:CYS152 4.9 18.1 1.0 O C:CYS152 5.0 18.1 1.0 C C:SER151 5.0 17.9 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 RAMP2 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 RAMP2 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1212 b:38.8 occ:1.00 SG C:CYS187 2.3 19.5 1.0 SG C:CYS177 2.4 29.1 1.0 SG C:CYS171 2.4 26.3 1.0 SG C:CYS190 2.5 24.2 1.0 CB C:CYS171 3.2 21.1 1.0 CB C:CYS187 3.2 17.9 1.0 CB C:CYS190 3.4 15.2 1.0 CB C:CYS177 3.4 28.1 1.0 N C:CYS177 4.1 30.2 1.0 CA C:CYS171 4.1 27.1 1.0 NE2 D:GLN210 4.2 59.4 1.0 N C:CYS190 4.2 17.2 1.0 O C:HOH2023 4.3 31.3 1.0 CA C:LYS175 4.3 31.1 1.0 CA C:CYS190 4.4 17.3 1.0 CA C:CYS177 4.4 25.7 1.0 N C:LYS175 4.4 30.4 1.0 N C:ASP176 4.6 40.6 1.0 CA C:CYS187 4.7 17.5 1.0 C C:LYS175 4.8 38.8 1.0 CB C:ASP173 4.8 39.9 1.0 C C:CYS171 4.9 35.8 1.0 OD2 C:ASP173 5.0 68.6 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 RAMP2 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 RAMP2 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1213 b:47.8 occ:1.00 SG D:CYS155 2.3 36.9 1.0 SG D:CYS135 2.4 36.2 1.0 SG D:CYS152 2.4 32.2 1.0 SG D:CYS138 2.4 36.4 1.0 CB D:CYS155 3.1 27.5 1.0 CB D:CYS135 3.3 39.9 1.0 CB D:CYS138 3.5 39.2 1.0 CB D:CYS152 3.7 27.6 1.0 N D:CYS138 3.7 38.8 1.0 N D:CYS155 4.0 25.9 1.0 N D:CYS152 4.0 30.4 1.0 CA D:CYS155 4.1 24.2 1.0 CA D:CYS138 4.2 45.4 1.0 NH1 D:ARG184 4.3 53.1 1.0 CB D:ILE137 4.4 32.0 1.0 CA D:CYS152 4.4 32.6 1.0 CB D:ASP140 4.5 56.4 1.0 NH2 D:ARG191 4.6 27.1 1.0 C D:ILE137 4.7 38.0 1.0 CA D:CYS135 4.7 46.0 1.0 C D:CYS138 4.9 46.7 1.0 CA D:ILE137 4.9 33.2 1.0 CD D:ARG184 4.9 34.0 1.0 CG2 D:ILE137 4.9 28.1 1.0 N D:ILE137 5.0 35.8 1.0 N D:ASP140 5.0 43.5 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 RAMP2 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 RAMP2 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1214 b:59.9 occ:1.00 SG D:CYS187 2.4 39.0 1.0 SG D:CYS190 2.4 44.0 1.0 SG D:CYS177 2.5 48.4 1.0 SG D:CYS171 2.7 45.4 1.0 CB D:CYS177 3.3 62.3 1.0 CB D:CYS190 3.3 38.3 1.0 CB D:CYS187 3.3 35.5 1.0 CB D:CYS171 3.6 44.9 1.0 O D:HOH2013 3.7 39.0 1.0 OD1 D:ASP173 4.0 0.3 1.0 N D:CYS177 4.1 61.9 1.0 N D:CYS190 4.1 35.5 1.0 CA D:CYS171 4.3 45.9 1.0 CA D:CYS177 4.3 62.7 1.0 CA D:CYS190 4.3 32.6 1.0 CA D:LYS175 4.4 62.1 1.0 N D:LYS175 4.6 61.2 1.0 N D:ASP176 4.7 63.2 1.0 C D:LYS175 4.8 60.6 1.0 CA D:CYS187 4.8 32.7 1.0 N D:ARG172 4.9 52.7 1.0 CD1 D:TYR189 4.9 38.5 1.0 CG D:ASP173 5.0 0.4 1.0 CB D:TYR189 5.0 37.1 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