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Zinc in PDB 3e00: Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide

Protein crystallography data

The structure of Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3e00 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) 46.76 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.585, 146.775, 67.230, 90.00, 115.52, 90.00
R / Rfree (%) 21.4 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide (pdb code 3e00). 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 GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide, PDB code: 3e00:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3e00

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Zinc binding site 1 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 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 GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7221

b:81.0
occ:1.00
SG A:CYS152 2.3 63.4 1.0
SG A:CYS138 2.4 61.6 1.0
SG A:CYS135 2.5 87.3 1.0
SG A:CYS155 2.7 65.0 1.0
CB A:CYS152 3.0 63.4 1.0
CB A:CYS155 3.2 65.0 1.0
CB A:CYS135 3.3 87.3 1.0
N A:CYS152 3.5 67.7 1.0
CA A:CYS152 3.8 67.7 1.0
CB A:CYS138 3.9 61.6 1.0
NH1 A:ARG184 3.9 96.7 1.0
N A:CYS155 4.1 68.8 1.0
N A:CYS138 4.1 76.7 1.0
CA A:CYS155 4.3 68.8 1.0
O A:CYS152 4.4 67.7 1.0
CB A:ILE137 4.5 61.4 1.0
C A:CYS152 4.5 67.7 1.0
CB A:ASP140 4.5 85.0 1.0
CA A:CYS138 4.6 76.7 1.0
C A:SER151 4.7 70.0 1.0
NH2 A:ARG191 4.7 51.2 1.0
CA A:CYS135 4.8 75.1 1.0
C A:ILE137 4.9 73.7 1.0
CG2 A:ILE137 4.9 61.4 1.0
CA A:SER151 5.0 70.0 1.0
CZ A:ARG184 5.0 96.7 1.0

Zinc binding site 2 out of 4 in 3e00

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Zinc binding site 2 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 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 GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7222

b:69.7
occ:1.00
SG A:CYS171 2.3 83.1 1.0
SG A:CYS190 2.4 40.2 1.0
SG A:CYS177 2.5 80.3 1.0
SG A:CYS187 2.6 64.0 1.0
CB A:CYS171 3.3 83.1 1.0
CB A:CYS177 3.5 80.3 1.0
CB A:CYS187 3.6 64.0 1.0
CB A:CYS190 3.6 40.2 1.0
CA A:CYS171 4.0 64.9 1.0
CA A:LYS175 4.2 67.9 1.0
N A:CYS190 4.2 54.8 1.0
N A:LYS175 4.2 67.9 1.0
N A:CYS177 4.4 61.4 1.0
CA A:CYS190 4.5 54.8 1.0
CA A:CYS177 4.6 61.4 1.0
N A:ASP176 4.7 0.1 1.0
CD2 A:TYR189 4.7 74.7 1.0
C A:LYS175 4.8 67.9 1.0
C A:CYS171 4.8 64.9 1.0
N A:ARG172 4.8 78.1 1.0
CB A:ASP173 4.9 0.2 1.0
N A:ASP173 4.9 71.3 1.0
CB A:TYR189 5.0 74.7 1.0

Zinc binding site 3 out of 4 in 3e00

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Zinc binding site 3 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 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 GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7121

b:81.7
occ:1.00
SG D:CYS128 2.3 73.3 1.0
SG D:CYS114 2.4 83.2 1.0
SG D:CYS111 2.6 89.3 1.0
SG D:CYS131 2.6 58.9 1.0
CB D:CYS128 3.3 73.3 1.0
CB D:CYS111 3.4 89.3 1.0
CB D:CYS114 3.4 83.2 1.0
N D:CYS114 3.6 79.6 1.0
CB D:CYS131 3.7 58.9 1.0
N D:CYS128 3.8 60.8 1.0
CA D:CYS114 4.0 79.6 1.0
CA D:CYS128 4.2 60.8 1.0
NH2 D:ARG159 4.3 92.5 1.0
N D:CYS131 4.4 69.9 1.0
CB D:VAL113 4.4 64.7 1.0
N D:GLY115 4.5 77.1 1.0
CB D:ASP116 4.5 88.7 1.0
C D:VAL113 4.6 68.5 1.0
N D:ASP116 4.6 79.8 1.0
C D:CYS114 4.6 79.6 1.0
CA D:CYS131 4.7 69.9 1.0
N D:VAL113 4.7 68.5 1.0
CA D:VAL113 4.8 68.5 1.0
CA D:CYS111 4.8 82.7 1.0
O D:CYS128 4.9 60.8 1.0
C D:ALA127 5.0 70.1 1.0
CZ D:ARG159 5.0 92.5 1.0
C D:CYS128 5.0 60.8 1.0

Zinc binding site 4 out of 4 in 3e00

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Zinc binding site 4 out of 4 in the Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex on Dna Bound with GW9662, 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 GW9662, 9-Cis Retinoic Acid and NCOA2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7122

b:83.9
occ:1.00
SG D:CYS152 2.4 82.4 1.0
SG D:CYS165 2.4 97.7 1.0
SG D:CYS162 2.6 0.8 1.0
SG D:CYS148 2.6 0.2 1.0
CB D:CYS162 3.3 0.8 1.0
CB D:CYS148 3.4 0.2 1.0
CB D:CYS165 3.7 97.7 1.0
CB D:CYS152 3.7 82.4 1.0
O D:LEU150 3.8 0.4 1.0
O A:ARG211 4.4 94.2 1.0
N D:CYS165 4.4 78.1 1.0
CA D:CYS165 4.6 78.1 1.0
CA D:CYS148 4.8 98.0 1.0
CA D:CYS162 4.8 0.4 1.0
N D:CYS152 4.9 96.7 1.0
O D:CYS148 4.9 98.0 1.0
C D:CYS148 4.9 98.0 1.0
C D:LEU150 4.9 0.4 1.0
CA D:CYS152 4.9 96.7 1.0

Reference:

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
Page generated: Sat Sep 26 06:06:43 2020
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