Zinc in PDB 3dzu: Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide

The structure of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3dzu 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)	38.93 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.186, 66.907, 78.464, 70.95, 82.56, 62.88
R / Rfree (%)	20.1 / 27.2

The structure of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide (pdb code 3dzu). 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 Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3dzu:
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 Bvt.13, 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 Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7221 b:74.4 occ:1.00 SG A:CYS138 2.3 74.8 1.0 SG A:CYS152 2.4 95.7 1.0 SG A:CYS135 2.4 82.4 1.0 SG A:CYS155 2.6 74.6 1.0 CB A:CYS135 2.9 82.7 1.0 CB A:CYS152 3.3 95.9 1.0 CB A:CYS155 3.4 73.1 1.0 N A:CYS152 3.7 67.1 1.0 CB A:CYS138 3.9 75.2 1.0 N A:CYS155 4.0 68.5 1.0 N A:CYS138 4.0 83.5 1.0 CA A:CYS152 4.0 66.4 1.0 NH1 A:ARG184 4.3 58.1 1.0 CA A:CYS155 4.3 68.4 1.0 CB A:ASP140 4.4 76.5 1.0 CA A:CYS135 4.4 79.8 1.0 CA A:CYS138 4.5 83.8 1.0 CB A:ILE137 4.6 70.3 1.0 O A:CYS152 4.6 65.7 1.0 C A:CYS152 4.7 65.7 1.0 N A:GLY139 4.7 88.0 1.0 N A:ASP140 4.8 48.9 1.0 C A:SER151 4.8 62.4 1.0 CG2 A:ILE137 4.8 70.4 1.0 CB A:SER151 4.9 92.7 1.0 CA A:SER151 5.0 63.2 1.0

Zinc binding site 2 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 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 Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7222 b:69.9 occ:1.00 SG A:CYS171 2.2 67.2 1.0 SG A:CYS190 2.4 61.5 1.0 SG A:CYS187 2.5 59.3 1.0 SG A:CYS177 2.6 63.5 1.0 CB A:CYS171 3.2 67.4 1.0 CB A:CYS190 3.3 60.7 1.0 CB A:CYS187 3.4 59.9 1.0 CB A:CYS177 3.5 64.1 1.0 N A:CYS190 4.0 49.3 1.0 CA A:CYS171 4.1 79.5 1.0 CA A:CYS190 4.2 48.9 1.0 CA A:LYS175 4.3 0.6 1.0 N A:CYS177 4.4 78.5 1.0 N A:LYS175 4.5 0.4 1.0 CD2 A:TYR189 4.6 57.0 1.0 CA A:CYS177 4.6 78.5 1.0 N A:ASP176 4.8 78.3 1.0 CA A:CYS187 4.8 83.4 1.0 CB A:TYR189 4.9 55.9 1.0 C A:CYS171 4.9 80.8 1.0

Zinc binding site 3 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 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 Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn7121 b:70.1 occ:1.00 SG D:CYS114 2.3 75.9 1.0 SG D:CYS131 2.4 54.1 1.0 SG D:CYS111 2.4 80.7 1.0 SG D:CYS128 2.4 58.0 1.0 CB D:CYS114 3.1 75.7 1.0 N D:CYS114 3.1 79.0 1.0 CB D:CYS131 3.1 55.1 1.0 CB D:CYS128 3.2 59.8 1.0 CB D:CYS111 3.3 79.5 1.0 CA D:CYS114 3.6 78.0 1.0 N D:CYS128 3.6 67.2 1.0 N D:GLY115 3.9 76.8 1.0 CA D:CYS128 4.0 66.1 1.0 C D:CYS114 4.2 77.3 1.0 CB D:VAL113 4.2 86.8 1.0 N D:CYS131 4.3 63.8 1.0 C D:VAL113 4.3 96.2 1.0 CA D:CYS131 4.3 64.1 1.0 OD1 D:ASP116 4.3 61.3 1.0 CA D:VAL113 4.6 96.9 1.0 N D:VAL113 4.7 97.5 1.0 C D:ALA127 4.7 73.5 1.0 CG1 D:VAL113 4.7 86.5 1.0 CA D:CYS111 4.7 87.0 1.0 C D:CYS128 4.8 65.8 1.0 O D:CYS128 4.8 65.4 1.0 CB D:ALA127 4.9 94.0 1.0 CA D:ALA127 4.9 74.2 1.0 NH2 D:ARG159 4.9 67.3 1.0 NH2 D:ARG166 5.0 48.3 1.0 C D:CYS111 5.0 86.5 1.0

Zinc binding site 4 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with Bvt.13, 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 Bvt.13, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn7122 b:83.1 occ:1.00 SG D:CYS165 2.4 0.6 1.0 SG D:CYS152 2.4 81.0 1.0 SG D:CYS162 2.4 74.8 1.0 SG D:CYS148 2.5 92.4 1.0 CB D:CYS152 3.0 81.1 1.0 CB D:CYS162 3.1 75.1 1.0 O D:LEU150 3.3 0.5 1.0 CB D:CYS165 3.4 0.1 1.0 CB D:CYS148 3.4 93.1 1.0 N D:CYS152 4.0 65.5 1.0 CA D:CYS152 4.1 65.3 1.0 N D:CYS165 4.3 61.1 1.0 CA D:CYS165 4.4 61.0 1.0 C D:LEU150 4.5 0.3 1.0 CA D:CYS162 4.6 71.8 1.0 CB D:LEU150 4.8 70.5 1.0 CA D:CYS148 4.9 78.5 1.0 C D:CYS162 5.0 71.6 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