Zinc in PDB 3dzy: Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide

The structure of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3dzy was solved by V.Chandra, P.Huang, Y.Hamuro, S.Raghuram, Y.Wang, T.P.Burris, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.71 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.803, 146.514, 67.223, 90.00, 115.59, 90.00
R / Rfree (%)	21.3 / 26.8

The binding sites of Zinc atom in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide (pdb code 3dzy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3dzy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7221 b:60.4 occ:1.00 SG A:CYS152 2.3 47.0 1.0 SG A:CYS135 2.4 51.8 1.0 SG A:CYS138 2.4 51.4 1.0 SG A:CYS155 2.7 55.7 1.0 CB A:CYS152 3.1 47.0 1.0 CB A:CYS135 3.3 51.8 1.0 CB A:CYS155 3.4 55.7 1.0 N A:CYS152 3.5 47.2 1.0 CB A:CYS138 3.6 51.4 1.0 N A:CYS138 3.7 82.2 1.0 NH1 A:ARG184 3.8 50.3 1.0 CA A:CYS152 3.9 47.2 1.0 CA A:CYS138 4.3 82.2 1.0 N A:CYS155 4.3 57.9 1.0 CB A:ILE137 4.3 37.0 1.0 CG2 A:ILE137 4.4 37.0 1.0 CA A:CYS155 4.5 57.9 1.0 O A:CYS152 4.6 47.2 1.0 C A:SER151 4.6 51.8 1.0 C A:CYS152 4.6 47.2 1.0 CB A:ASP140 4.6 71.4 1.0 C A:ILE137 4.7 66.3 1.0 CA A:CYS135 4.8 52.0 1.0 CA A:SER151 4.8 51.8 1.0 CA A:ILE137 4.9 66.3 1.0 N A:ILE137 4.9 66.3 1.0 N A:GLY139 5.0 72.2 1.0

Zinc binding site 2 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7222 b:52.8 occ:1.00 SG A:CYS190 2.3 38.3 1.0 SG A:CYS171 2.4 62.8 1.0 SG A:CYS187 2.5 52.1 1.0 SG A:CYS177 2.6 89.3 1.0 CB A:CYS177 3.0 89.3 1.0 CB A:CYS190 3.4 38.3 1.0 CB A:CYS187 3.4 52.1 1.0 CB A:CYS171 3.5 62.8 1.0 N A:CYS177 3.9 62.8 1.0 CA A:CYS177 4.0 62.8 1.0 N A:CYS190 4.1 36.1 1.0 CA A:CYS171 4.2 41.0 1.0 CA A:CYS190 4.3 36.1 1.0 CA A:LYS175 4.4 80.0 1.0 N A:ASP176 4.6 0.6 1.0 N A:LYS175 4.6 80.0 1.0 N A:ARG172 4.6 82.5 1.0 CD2 A:TYR189 4.7 60.6 1.0 C A:LYS175 4.7 80.0 1.0 CB A:ASP173 4.8 0.4 1.0 N A:ASP173 4.8 49.3 1.0 CA A:CYS187 4.8 68.5 1.0 C A:CYS171 5.0 41.0 1.0 CB A:TYR189 5.0 60.6 1.0

Zinc binding site 3 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn7121 b:63.6 occ:1.00 SG D:CYS114 2.3 51.6 1.0 SG D:CYS111 2.4 72.8 1.0 SG D:CYS131 2.4 50.6 1.0 SG D:CYS128 2.5 51.2 1.0 CB D:CYS131 3.0 50.6 1.0 CB D:CYS128 3.3 51.2 1.0 CB D:CYS111 3.4 72.8 1.0 N D:CYS114 3.5 64.0 1.0 CB D:CYS114 3.5 51.6 1.0 N D:CYS128 3.7 46.6 1.0 CA D:CYS114 4.0 64.0 1.0 N D:CYS131 4.0 66.3 1.0 CB D:VAL113 4.1 54.1 1.0 CA D:CYS128 4.1 46.6 1.0 CA D:CYS131 4.1 66.3 1.0 OD1 D:ASP116 4.2 76.8 1.0 N D:GLY115 4.4 59.0 1.0 C D:VAL113 4.4 66.8 1.0 NH2 D:ARG159 4.5 53.4 1.0 CA D:VAL113 4.6 66.8 1.0 N D:VAL113 4.7 66.8 1.0 CG2 D:VAL113 4.7 54.1 1.0 C D:CYS114 4.8 64.0 1.0 C D:CYS128 4.8 46.6 1.0 CA D:CYS111 4.8 68.2 1.0 C D:ALA127 4.8 53.1 1.0 O D:CYS128 4.8 46.6 1.0 NE D:ARG159 4.9 53.4 1.0 CZ D:ARG159 4.9 53.4 1.0 CG1 D:VAL113 5.0 54.1 1.0

Zinc binding site 4 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Rosiglitazone, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn7122 b:65.4 occ:1.00 SG D:CYS152 2.5 67.2 1.0 SG D:CYS162 2.6 79.2 1.0 SG D:CYS148 2.6 95.4 1.0 SG D:CYS165 2.7 74.6 1.0 CB D:CYS165 2.8 74.6 1.0 CB D:CYS148 3.1 95.4 1.0 CB D:CYS162 3.2 79.2 1.0 O D:LEU150 3.6 0.5 1.0 CB D:CYS152 3.7 67.2 1.0 CA D:CYS165 4.0 67.8 1.0 N D:CYS165 4.2 67.8 1.0 N D:CYS152 4.4 83.5 1.0 CA D:CYS148 4.5 78.5 1.0 C D:LEU150 4.6 0.5 1.0 CA D:CYS162 4.7 91.4 1.0 CA D:CYS152 4.7 83.5 1.0 O D:CYS148 4.7 78.5 1.0 C D:CYS148 4.8 78.5 1.0 CB D:LEU150 4.8 80.2 1.0

V.Chandra, P.Huang, Y.Hamuro, S.Raghuram, Y.Wang, T.P.Burris, F.Rastinejad. Structure of the Intact Ppar-Gamma-Rxr- Nuclear Receptor Complex on Dna. Nature V. 456 350 2008.
ISSN: ISSN 0028-0836
PubMed: 19043829
DOI: 10.1038/NATURE07413