Zinc in PDB 1ynw: Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element

The structure of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element, PDB code: 1ynw was solved by P.L.Shaffer, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.104, 57.049, 73.438, 90.00, 110.31, 90.00
R / Rfree (%)	23.2 / 28.3

The binding sites of Zinc atom in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element (pdb code 1ynw). 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 Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element, PDB code: 1ynw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 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 Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:92.9 occ:1.00 SG A:CYS24 2.5 0.9 1.0 SG A:CYS44 2.5 94.2 1.0 SG A:CYS41 2.6 81.5 1.0 SG A:CYS27 2.7 0.3 1.0 CB A:CYS41 3.2 84.4 1.0 CB A:CYS44 3.2 92.6 1.0 CB A:CYS24 3.3 0.7 1.0 CB A:CYS27 3.6 0.5 1.0 N A:CYS27 3.6 0.1 1.0 N A:CYS41 3.6 84.3 1.0 CB A:VAL26 4.0 0.9 1.0 CA A:CYS41 4.0 83.9 1.0 CA A:CYS27 4.1 0.4 1.0 CG1 A:VAL26 4.1 0.3 1.0 N A:CYS44 4.2 90.8 1.0 CA A:CYS44 4.3 92.6 1.0 CB A:ASP29 4.5 97.8 1.0 C A:VAL26 4.6 0.6 1.0 CA A:VAL26 4.7 0.9 1.0 CA A:CYS24 4.7 0.2 1.0 O A:CYS41 4.7 82.8 1.0 N A:VAL26 4.7 0.8 1.0 C A:CYS27 4.7 0.8 1.0 C A:CYS41 4.7 83.3 1.0 C A:THR40 4.8 85.2 1.0 NH1 A:ARG73 4.8 95.3 1.0 NH2 A:ARG80 4.9 88.9 1.0 CB A:THR40 5.0 85.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 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 Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:0.6 occ:1.00 SG A:CYS66 2.3 0.3 1.0 SG A:CYS76 2.4 94.3 1.0 SG A:CYS79 2.4 0.3 1.0 SG A:CYS60 2.4 0.3 1.0 CB A:CYS60 2.7 0.3 1.0 CB A:CYS79 3.3 97.8 1.0 CB A:CYS76 3.6 97.1 1.0 N A:ASP65 3.8 0.8 1.0 N A:CYS66 3.9 0.8 1.0 CA A:CYS60 3.9 0.2 1.0 CB A:CYS66 4.0 0.7 1.0 CA A:GLY64 4.1 0.1 1.0 N A:CYS79 4.2 94.3 1.0 C A:GLY64 4.3 0.1 1.0 CA A:CYS79 4.3 96.0 1.0 N A:GLY64 4.5 0.9 1.0 CA A:CYS66 4.6 0.5 1.0 C A:CYS60 4.6 0.4 1.0 CB A:ALA62 4.6 0.6 1.0 CA A:ASP65 4.7 0.1 1.0 C A:ASP65 4.8 0.6 1.0 CA A:CYS76 5.0 97.8 1.0 N A:CYS60 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 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 Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:99.7 occ:1.00 SG B:CYS255 2.2 89.4 1.0 SG B:CYS235 2.4 0.1 1.0 SG B:CYS238 2.5 0.5 1.0 SG B:CYS252 2.6 93.1 1.0 N B:CYS238 3.0 0.5 1.0 CB B:CYS238 3.1 0.6 1.0 CB B:CYS255 3.2 93.7 1.0 CB B:CYS235 3.3 0.6 1.0 CA B:CYS238 3.5 0.7 1.0 CB B:CYS252 3.6 94.6 1.0 N B:CYS252 3.9 94.8 1.0 CB B:ILE237 3.9 0.7 1.0 C B:ILE237 4.1 0.3 1.0 N B:GLY239 4.2 0.0 1.0 C B:CYS238 4.2 0.9 1.0 N B:CYS255 4.2 94.6 1.0 CA B:CYS255 4.3 94.1 1.0 CA B:CYS252 4.3 93.6 1.0 CA B:ILE237 4.5 0.6 1.0 NH2 B:ARG291 4.5 89.1 1.0 CA B:CYS235 4.7 0.7 1.0 N B:ILE237 4.7 0.8 1.0 CG1 B:ILE237 4.7 0.3 1.0 CG2 B:ILE237 4.8 0.0 1.0 NH1 B:ARG284 4.8 97.6 1.0 O B:CYS235 4.9 0.6 1.0 C B:SER251 4.9 96.3 1.0 C B:CYS235 5.0 0.7 1.0 N B:ASP240 5.0 0.5 1.0 CB B:ASP240 5.0 0.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 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 Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn351 b:0.6 occ:1.00 SG B:CYS287 2.2 0.9 1.0 SG B:CYS277 2.5 0.5 1.0 SG B:CYS271 2.6 0.5 1.0 CB B:CYS287 2.7 0.2 1.0 SG B:CYS290 2.8 0.6 1.0 CB B:CYS271 3.8 0.1 1.0 CB B:CYS290 3.8 0.4 1.0 CB B:CYS277 3.9 0.8 1.0 CA B:CYS271 3.9 0.4 1.0 N B:ARG272 3.9 0.8 1.0 CA B:CYS287 4.2 0.8 1.0 C B:CYS271 4.4 0.4 1.0 N B:CYS290 4.5 0.1 1.0 N B:ASP273 4.5 0.6 1.0 CA B:CYS290 4.8 0.8 1.0 C B:CYS287 4.8 0.7 1.0 O B:CYS287 4.9 0.9 1.0 CA B:LYS275 4.9 0.5 1.0 N B:LYS275 4.9 0.3 1.0 CA B:ARG272 4.9 0.9 1.0 CB B:ARG272 4.9 0.3 1.0 CD2 B:TYR289 5.0 0.1 1.0 CB B:TYR289 5.0 0.2 1.0

P.L.Shaffer, D.T.Gewirth. Structural Analysis of Rxr-Vdr Interactions on DR3 Dna J.Steroid Biochem.Mol.Biol. V.9-90 215 2004.
ISSN: ISSN 0960-0760
PubMed: 15225774
DOI: 10.1016/J.JSBMB.2004.03.084