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Zinc in PDB 1by4: Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna

Protein crystallography data

The structure of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna, PDB code: 1by4 was solved by Q.Zhao, S.A.Chasse, S.Devarakonda, M.L.Sierk, B.Ahvazi, P.B.Sigler, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.930, 33.650, 101.400, 90.00, 89.95, 90.00
R / Rfree (%) 23.4 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna (pdb code 1by4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna, PDB code: 1by4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1by4

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Zinc binding site 1 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1330

b:24.4
occ:1.00
 SG A:CYS1155 2.2 18.1 1.0
SG A:CYS1152 2.3 25.5 1.0
SG A:CYS1135 2.4 21.8 1.0
SG A:CYS1138 2.5 20.7 1.0
CB A:CYS1155 3.2 19.2 1.0
CB A:CYS1135 3.4 17.6 1.0
CB A:CYS1138 3.5 13.1 1.0
CB A:CYS1152 3.7 27.4 1.0
N A:CYS1152 4.0 27.8 1.0
N A:CYS1155 4.0 17.0 1.0
N A:CYS1138 4.1 19.4 1.0
NH1 A:ARG1184 4.1 24.6 1.0
CA A:CYS1155 4.3 21.5 1.0
CA A:CYS1138 4.3 11.3 1.0
CA A:CYS1152 4.4 25.9 1.0
CB A:ASP1140 4.4 22.4 1.0
CD A:ARG1184 4.5 28.6 1.0
O A:CYS1152 4.6 20.9 1.0
C A:ILE1137 4.6 29.3 1.0
CZ A:ARG1184 4.7 30.9 1.0
CB A:ILE1137 4.7 28.4 1.0
C A:CYS1152 4.8 17.8 1.0
CA A:CYS1135 4.8 29.2 1.0
NE A:ARG1184 4.8 34.6 1.0
C A:CYS1138 4.9 14.0 1.0
N A:ASP1140 4.9 22.5 1.0
NH2 A:ARG1191 4.9 20.3 1.0
CA A:ILE1137 5.0 30.0 1.0

Zinc binding site 2 out of 8 in 1by4

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Zinc binding site 2 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1331

b:45.1
occ:1.00
 SG A:CYS1190 2.3 37.0 1.0
SG A:CYS1177 2.4 51.6 1.0
SG A:CYS1187 2.4 49.0 1.0
SG A:CYS1171 2.4 48.5 1.0
CB A:CYS1187 3.3 37.1 1.0
CB A:CYS1177 3.3 45.6 1.0
CB A:CYS1190 3.3 38.6 1.0
O A:ASN1174 3.8 49.0 1.0
CB A:CYS1171 3.8 55.6 1.0
N A:CYS1190 4.1 35.4 1.0
N A:CYS1177 4.2 41.9 1.0
CA A:CYS1171 4.3 59.1 1.0
CA A:CYS1190 4.3 38.2 1.0
N A:ASP1176 4.4 42.5 1.0
CA A:CYS1177 4.4 40.7 1.0
C A:ASN1174 4.4 53.9 1.0
CA A:LYS1175 4.5 47.3 1.0
N A:LYS1175 4.7 49.8 1.0
CD2 A:TYR1189 4.7 25.8 1.0
CB A:TYR1189 4.7 37.5 1.0
CA A:CYS1187 4.8 40.1 1.0
N A:ASN1174 4.9 63.5 1.0
C A:LYS1175 5.0 44.6 1.0

Zinc binding site 3 out of 8 in 1by4

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Zinc binding site 3 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1335

b:20.9
occ:1.00
 SG B:CYS1252 2.3 18.1 1.0
SG B:CYS1235 2.3 13.7 1.0
SG B:CYS1255 2.4 21.5 1.0
SG B:CYS1238 2.5 15.0 1.0
CB B:CYS1252 3.3 15.9 1.0
CB B:CYS1235 3.3 13.4 1.0
CB B:CYS1255 3.4 15.7 1.0
CB B:CYS1238 3.7 4.7 1.0
N B:CYS1252 3.7 12.9 1.0
N B:CYS1238 3.8 19.7 1.0
N B:CYS1255 4.0 18.0 1.0
NH1 B:ARG1284 4.0 13.6 1.0
CA B:CYS1252 4.1 16.3 1.0
CA B:CYS1238 4.3 15.8 1.0
CB B:ASP1240 4.3 9.8 1.0
CA B:CYS1255 4.3 20.8 1.0
CB B:ILE1237 4.4 17.2 1.0
O B:CYS1252 4.7 22.0 1.0
C B:CYS1252 4.7 18.0 1.0
CA B:CYS1235 4.8 8.7 1.0
C B:ILE1237 4.8 22.0 1.0
N B:ASP1240 4.9 22.2 1.0
CZ B:ARG1284 4.9 9.1 1.0
C B:CYS1238 4.9 19.0 1.0
C B:SER1251 4.9 17.7 1.0
N B:GLY1239 4.9 25.3 1.0
CA B:ILE1237 5.0 20.7 1.0
CD1 B:ILE1237 5.0 13.3 1.0
C B:GLY1254 5.0 25.2 1.0

Zinc binding site 4 out of 8 in 1by4

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Zinc binding site 4 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1336

b:28.7
occ:1.00
 SG B:CYS1287 2.2 12.7 1.0
SG B:CYS1271 2.3 35.0 1.0
SG B:CYS1290 2.3 20.4 1.0
SG B:CYS1277 2.4 31.0 1.0
CB B:CYS1287 3.2 20.3 1.0
CB B:CYS1277 3.3 39.2 1.0
CB B:CYS1290 3.3 14.5 1.0
CB B:CYS1271 3.4 37.9 1.0
N B:CYS1290 3.9 19.7 1.0
O B:ASN1274 3.9 25.8 1.0
O B:LYS1275 4.0 41.7 1.0
CA B:CYS1271 4.0 36.5 1.0
CA B:CYS1290 4.2 21.3 1.0
CD2 B:TYR1289 4.2 22.4 1.0
OE2 C:GLU2207 4.4 62.7 1.0
O B:CYS1287 4.5 26.1 1.0
CA B:CYS1277 4.5 38.0 1.0
CA B:CYS1287 4.5 25.4 1.0
N B:CYS1277 4.6 42.3 1.0
CB B:TYR1289 4.6 15.7 1.0
N B:ARG1272 4.7 39.3 1.0
C B:CYS1271 4.8 36.8 1.0
CB B:ASP1273 4.9 50.3 1.0
C B:TYR1289 4.9 20.8 1.0
C B:ASP1276 4.9 44.7 1.0
C B:CYS1287 4.9 27.1 1.0
N B:ASN1274 4.9 40.0 1.0
CG B:TYR1289 4.9 21.0 1.0
C B:LYS1275 4.9 40.8 1.0
C B:ASN1274 5.0 33.5 1.0

Zinc binding site 5 out of 8 in 1by4

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Zinc binding site 5 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2330

b:28.0
occ:1.00
 SG C:CYS2155 2.1 13.2 1.0
SG C:CYS2152 2.3 33.2 1.0
SG C:CYS2135 2.4 18.2 1.0
SG C:CYS2138 2.4 28.3 1.0
CB C:CYS2138 3.2 22.1 1.0
CB C:CYS2155 3.2 17.8 1.0
CB C:CYS2135 3.3 19.3 1.0
CB C:CYS2152 3.6 29.4 1.0
N C:CYS2155 3.8 20.6 1.0
NH1 C:ARG2184 3.8 29.4 1.0
N C:CYS2138 3.9 14.2 1.0
N C:CYS2152 4.1 24.7 1.0
CA C:CYS2138 4.1 18.8 1.0
CA C:CYS2155 4.1 21.7 1.0
CB C:ASP2140 4.3 28.3 1.0
CA C:CYS2152 4.4 25.4 1.0
C C:ILE2137 4.4 18.4 1.0
NH2 C:ARG2191 4.5 12.5 1.0
CB C:ILE2137 4.6 19.4 1.0
CA C:CYS2135 4.7 26.2 1.0
C C:CYS2138 4.8 17.6 1.0
C C:GLY2154 4.9 19.2 1.0
N C:ASP2140 4.9 27.1 1.0
N C:GLY2139 4.9 24.6 1.0
N C:ILE2137 4.9 28.0 1.0
CD C:ARG2184 4.9 22.5 1.0
CA C:ILE2137 4.9 21.2 1.0
CZ C:ARG2184 5.0 31.9 1.0

Zinc binding site 6 out of 8 in 1by4

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Zinc binding site 6 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2331

b:43.3
occ:1.00
 SG C:CYS2177 2.3 52.3 1.0
SG C:CYS2187 2.4 47.8 1.0
SG C:CYS2171 2.4 53.7 1.0
SG C:CYS2190 2.4 45.2 1.0
CB C:CYS2187 3.0 32.5 1.0
CB C:CYS2177 3.0 52.0 1.0
CB C:CYS2171 3.3 52.6 1.0
CB C:CYS2190 3.4 39.9 1.0
O C:ASP2176 3.4 62.2 1.0
C C:ASP2176 3.9 56.6 1.0
CA C:CYS2171 3.9 56.7 1.0
CA C:CYS2177 4.2 49.3 1.0
C C:LYS2175 4.3 48.3 1.0
N C:CYS2177 4.3 49.5 1.0
N C:ASP2176 4.3 50.8 1.0
N C:CYS2190 4.3 31.6 1.0
CA C:CYS2187 4.4 33.1 1.0
CA C:LYS2175 4.5 51.9 1.0
CA C:CYS2190 4.5 32.1 1.0
O C:HOH3184 4.5 49.4 1.0
CD2 C:TYR2189 4.6 26.5 1.0
O C:LYS2175 4.6 40.0 1.0
N C:ARG2172 4.7 61.5 1.0
CA C:ASP2176 4.8 56.9 1.0
C C:CYS2171 4.8 59.8 1.0
N C:LYS2175 4.9 58.3 1.0

Zinc binding site 7 out of 8 in 1by4

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Zinc binding site 7 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2335

b:23.9
occ:1.00
 SG D:CYS2252 2.3 16.1 1.0
SG D:CYS2235 2.3 20.4 1.0
SG D:CYS2255 2.4 25.6 1.0
SG D:CYS2238 2.5 18.3 1.0
CB D:CYS2235 3.2 22.5 1.0
CB D:CYS2255 3.3 28.1 1.0
CB D:CYS2252 3.4 20.6 1.0
CB D:CYS2238 3.5 14.0 1.0
N D:CYS2252 3.7 24.2 1.0
N D:CYS2238 3.8 21.6 1.0
N D:CYS2255 3.9 22.5 1.0
NH1 D:ARG2284 4.0 14.4 1.0
CG1 D:ILE2237 4.1 25.8 1.0
CB D:ASP2240 4.1 23.6 1.0
CA D:CYS2252 4.2 18.6 1.0
CA D:CYS2238 4.2 18.4 1.0
CA D:CYS2255 4.2 23.2 1.0
CA D:CYS2235 4.7 17.4 1.0
O D:CYS2252 4.7 15.9 1.0
C D:CYS2252 4.8 22.5 1.0
N D:ASP2240 4.8 25.4 1.0
C D:ILE2237 4.8 15.8 1.0
CZ D:ARG2284 4.8 14.4 1.0
NH1 D:ARG2291 4.8 18.2 1.0
C D:CYS2238 4.8 19.0 1.0
C D:SER2251 4.9 25.2 1.0
N D:GLY2239 4.9 19.3 1.0
OD2 D:ASP2240 4.9 22.2 1.0
C D:GLY2254 5.0 28.4 1.0
CB D:ILE2237 5.0 22.0 1.0

Zinc binding site 8 out of 8 in 1by4

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Zinc binding site 8 out of 8 in the Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure and Mechanism of the Homodimeric Assembly of the Rxr on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2336

b:27.5
occ:1.00
 SG D:CYS2287 2.2 16.3 1.0
SG D:CYS2271 2.3 39.1 1.0
SG D:CYS2277 2.3 34.5 1.0
SG D:CYS2290 2.5 21.2 1.0
CB D:CYS2277 3.2 34.4 1.0
CB D:CYS2290 3.2 20.4 1.0
CB D:CYS2287 3.3 25.9 1.0
CB D:CYS2271 3.4 23.0 1.0
CA D:CYS2271 3.9 26.6 1.0
N D:CYS2290 4.0 26.1 1.0
N D:CYS2277 4.2 37.3 1.0
CA D:CYS2290 4.2 23.0 1.0
CA D:CYS2277 4.3 34.1 1.0
CD2 D:TYR2289 4.4 25.4 1.0
O D:LYS2275 4.5 37.9 1.0
CA D:CYS2287 4.7 28.5 1.0
O D:ASN2274 4.7 31.7 1.0
O D:CYS2287 4.7 26.3 1.0
C D:CYS2271 4.8 27.4 1.0
N D:ARG2272 4.8 28.4 1.0
CB D:TYR2289 4.9 16.2 1.0
CB D:ASP2273 4.9 44.5 1.0
C D:CYS2287 5.0 24.2 1.0
N D:ASP2273 5.0 31.6 1.0

Reference:

Q.Zhao, S.A.Chasse, S.Devarakonda, M.L.Sierk, B.Ahvazi, F.Rastinejad. Structural Basis of Rxr-Dna Interactions. J.Mol.Biol. V. 296 509 2000.
ISSN: ISSN 0022-2836
PubMed: 10669605
DOI: 10.1006/JMBI.1999.3457
Page generated: Sat Oct 12 22:47:36 2024

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