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Zinc in PDB 1dsz: Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1

Protein crystallography data

The structure of Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1, PDB code: 1dsz was solved by F.Rastinejad, T.Wagner, Q.Zhao, S.Khorasanizadeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.660, 33.900, 101.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1 (pdb code 1dsz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1, PDB code: 1dsz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1dsz

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Zinc binding site 1 out of 4 in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1121

b:17.0
occ:1.00
SG A:CYS1155 2.3 16.5 1.0
SG A:CYS1138 2.3 17.6 1.0
SG A:CYS1135 2.3 16.3 1.0
SG A:CYS1152 2.4 15.8 1.0
CB A:CYS1155 3.2 16.7 1.0
CB A:CYS1135 3.2 16.0 1.0
CB A:CYS1138 3.2 20.5 1.0
CB A:CYS1152 3.6 19.4 1.0
N A:CYS1138 3.7 21.1 1.0
N A:CYS1152 4.0 16.2 1.0
CA A:CYS1138 4.1 22.1 1.0
N A:CYS1155 4.2 13.9 1.0
CA A:CYS1155 4.3 12.2 1.0
CA A:CYS1152 4.3 18.4 1.0
NH1 A:ARG1184 4.4 18.2 1.0
CB A:VAL1137 4.4 18.0 1.0
CB A:ASP1140 4.6 23.5 1.0
C A:CYS1138 4.6 20.9 1.0
C A:VAL1137 4.7 23.3 1.0
CA A:CYS1135 4.7 17.6 1.0
N A:GLN1139 4.8 19.6 1.0
N A:ASP1140 4.8 21.9 1.0
NH2 A:ARG1191 4.8 11.6 1.0
CD A:ARG1184 4.8 10.9 1.0
O A:CYS1152 4.9 16.2 1.0
C A:CYS1152 4.9 13.5 1.0
CA A:VAL1137 5.0 21.8 1.0
N A:VAL1137 5.0 27.2 1.0

Zinc binding site 2 out of 4 in 1dsz

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Zinc binding site 2 out of 4 in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1122

b:22.4
occ:1.00
SG A:CYS1171 2.3 25.7 1.0
SG A:CYS1177 2.3 24.7 1.0
SG A:CYS1187 2.3 20.1 1.0
SG A:CYS1190 2.4 23.6 1.0
CB A:CYS1177 3.1 25.4 1.0
CB A:CYS1187 3.3 22.1 1.0
CB A:CYS1190 3.3 21.6 1.0
CB A:CYS1171 3.5 22.8 1.0
N A:CYS1177 4.0 32.7 1.0
O A:HOH2128 4.1 28.6 1.0
N A:CYS1190 4.2 20.1 1.0
CA A:CYS1177 4.2 27.8 1.0
O A:HOH2160 4.3 27.8 1.0
CA A:CYS1171 4.3 30.2 1.0
CA A:LYS1175 4.3 25.5 1.0
N A:LYS1175 4.3 26.3 1.0
CA A:CYS1190 4.3 22.2 1.0
N A:ASN1176 4.6 18.5 1.0
C A:LYS1175 4.7 23.5 1.0
CA A:CYS1187 4.8 21.2 1.0
CD2 A:TYR1189 4.8 26.5 1.0
CB A:TYR1189 4.9 18.3 1.0

Zinc binding site 3 out of 4 in 1dsz

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Zinc binding site 3 out of 4 in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1221

b:9.9
occ:1.00
SG B:CYS1235 2.3 9.3 1.0
SG B:CYS1252 2.3 10.5 1.0
SG B:CYS1255 2.3 9.8 1.0
SG B:CYS1238 2.3 8.9 1.0
CB B:CYS1255 3.3 10.3 1.0
CB B:CYS1235 3.3 9.0 1.0
CB B:CYS1238 3.4 11.4 1.0
CB B:CYS1252 3.5 8.5 1.0
N B:CYS1238 3.8 8.9 1.0
N B:CYS1252 3.9 9.0 1.0
N B:CYS1255 4.1 9.2 1.0
CA B:CYS1238 4.1 11.3 1.0
NH1 B:ARG1284 4.2 11.5 1.0
CA B:CYS1255 4.3 7.4 1.0
CA B:CYS1252 4.3 8.7 1.0
CB B:ILE1237 4.4 7.4 1.0
CB B:ASP1240 4.5 9.5 1.0
C B:ILE1237 4.7 9.9 1.0
C B:CYS1238 4.7 11.6 1.0
NH2 B:ARG1291 4.7 10.1 1.0
CA B:CYS1235 4.7 7.9 1.0
N B:GLY1239 4.8 9.8 1.0
CD B:ARG1284 4.8 11.6 1.0
N B:ASP1240 4.8 8.3 1.0
CA B:ILE1237 4.9 7.3 1.0
C B:CYS1252 5.0 9.3 1.0
CG2 B:ILE1237 5.0 11.1 1.0
N B:ILE1237 5.0 9.1 1.0

Zinc binding site 4 out of 4 in 1dsz

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Zinc binding site 4 out of 4 in the Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Rxr/Rar Dna-Binding Domain Heterodimer in Complex with the Retinoic Acid Response Element DR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1222

b:15.2
occ:1.00
SG B:CYS1290 2.3 12.8 1.0
SG B:CYS1271 2.3 15.7 1.0
SG B:CYS1277 2.4 16.2 1.0
SG B:CYS1287 2.4 15.2 1.0
CB B:CYS1277 3.2 14.5 1.0
CB B:CYS1287 3.3 13.8 1.0
CB B:CYS1290 3.3 12.7 1.0
CB B:CYS1271 3.4 13.3 1.0
N B:CYS1277 4.0 17.4 1.0
CA B:CYS1271 4.2 15.1 1.0
N B:CYS1290 4.2 11.5 1.0
CA B:CYS1277 4.2 13.9 1.0
O B:HOH2063 4.3 20.2 1.0
CA B:CYS1290 4.3 9.1 1.0
O B:HOH2313 4.3 20.0 1.0
CA B:LYS1275 4.4 15.9 1.0
N B:LYS1275 4.5 19.0 1.0
N B:ASP1276 4.6 15.8 1.0
CD2 B:TYR1289 4.7 9.2 1.0
C B:LYS1275 4.7 12.6 1.0
CA B:CYS1287 4.7 10.5 1.0
CB B:TYR1289 4.9 9.1 1.0
C B:CYS1271 4.9 22.7 1.0
CB B:ASP1273 5.0 37.4 1.0
N B:ARG1272 5.0 19.5 1.0

Reference:

F.Rastinejad, T.Wagner, Q.Zhao, S.Khorasanizadeh. Structure of the Rxr-Rar Dna-Binding Complex on the Retinoic Acid Response Element DR1. Embo J. V. 19 1045 2000.
ISSN: ISSN 0261-4189
PubMed: 10698945
DOI: 10.1093/EMBOJ/19.5.1045
Page generated: Mon Jan 25 16:09:06 2021

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