Zinc in PDB 8hbm: Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna

Protein crystallography data

The structure of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna, PDB code: 8hbm was solved by L.Jiang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.57 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.65, 60.016, 241.797, 90, 90, 90
R / Rfree (%) 24.8 / 30.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna (pdb code 8hbm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna, PDB code: 8hbm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8hbm

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Zinc binding site 1 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:49.2
occ:1.00
 SG A:CYS138 2.3 52.1 1.0
SG A:CYS155 2.3 66.5 1.0
SG A:CYS152 2.3 64.8 1.0
SG A:CYS135 2.3 70.1 1.0
CB A:CYS155 3.3 60.5 1.0
CB A:CYS135 3.5 56.8 1.0
CB A:CYS138 3.6 73.7 1.0
CB A:CYS152 3.7 55.1 1.0
N A:CYS138 3.8 72.9 1.0
N A:CYS152 3.9 67.8 1.0
NH1 A:ARG184 4.0 66.7 1.0
N A:CYS155 4.0 66.2 1.0
CA A:CYS155 4.3 73.1 1.0
CA A:CYS138 4.3 55.2 1.0
CA A:CYS152 4.4 79.0 1.0
CB A:ILE137 4.4 75.7 1.0
CB A:ASP140 4.5 68.0 1.0
CG2 A:ILE137 4.8 81.3 1.0
N A:ASP140 4.8 53.6 1.0
C A:ILE137 4.8 81.8 1.0
N A:GLY139 4.9 67.9 1.0
CD A:ARG184 4.9 55.6 1.0
CA A:CYS135 4.9 64.1 1.0
C A:CYS138 4.9 55.6 1.0
NH2 A:ARG191 4.9 60.0 1.0
N A:ILE137 5.0 72.8 1.0
CA A:ILE137 5.0 74.0 1.0

Zinc binding site 2 out of 8 in 8hbm

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Zinc binding site 2 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:93.7
occ:1.00
 SG A:CYS177 2.3 97.9 1.0
SG A:CYS187 2.3 118.0 1.0
SG A:CYS171 2.3 130.1 1.0
SG A:CYS190 2.3 87.5 1.0
CB A:CYS187 3.1 106.6 1.0
CB A:CYS171 3.2 120.7 1.0
CB A:CYS177 3.3 104.1 1.0
CB A:CYS190 3.5 102.6 1.0
N A:CYS177 4.0 101.6 1.0
N A:CYS190 4.0 84.9 1.0
CA A:CYS171 4.1 113.8 1.0
CA A:LYS175 4.2 109.6 1.0
CA A:CYS177 4.3 101.7 1.0
CA A:CYS190 4.4 87.5 1.0
N A:ASP176 4.5 121.9 1.0
C A:LYS175 4.5 114.8 1.0
N A:LYS175 4.6 128.6 1.0
CA A:CYS187 4.6 110.9 1.0
N A:ARG172 4.7 138.4 1.0
CB A:TYR189 4.7 90.8 1.0
CD2 A:TYR189 4.8 84.5 1.0
C A:CYS171 4.8 132.9 1.0
N A:ASP173 4.9 124.2 1.0

Zinc binding site 3 out of 8 in 8hbm

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Zinc binding site 3 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:68.7
occ:1.00
 SG B:CYS147 2.3 83.0 1.0
SG B:CYS130 2.3 77.2 1.0
SG B:CYS144 2.3 84.7 1.0
SG B:CYS127 2.3 99.3 1.0
CB B:CYS147 3.2 69.2 1.0
CB B:CYS127 3.3 79.7 1.0
NH1 B:ARG176 3.5 135.2 1.0
CB B:CYS130 3.6 75.6 1.0
CB B:CYS144 3.6 98.3 1.0
N B:CYS130 3.8 82.6 1.0
N B:CYS144 4.0 97.7 1.0
N B:CYS147 4.0 67.6 1.0
CA B:CYS147 4.2 77.6 1.0
CA B:CYS130 4.3 72.3 1.0
CA B:CYS144 4.3 103.6 1.0
CB B:VAL129 4.4 77.1 1.0
CB B:ASP132 4.6 91.0 1.0
CA B:CYS127 4.7 86.9 1.0
N B:ASP132 4.8 82.1 1.0
CZ B:ARG176 4.8 79.8 1.0
C B:VAL129 4.8 93.6 1.0
N B:GLY131 4.8 81.2 1.0
C B:CYS130 4.9 73.4 1.0
C B:CYS144 4.9 98.2 1.0
O B:CYS144 4.9 98.1 1.0
CA B:VAL129 5.0 84.9 1.0
CG1 B:VAL129 5.0 88.6 1.0
N B:VAL129 5.0 90.9 1.0

Zinc binding site 4 out of 8 in 8hbm

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Zinc binding site 4 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:101.5
occ:1.00
 SG B:CYS179 2.3 59.5 1.0
SG B:CYS169 2.3 81.2 1.0
SG B:CYS163 2.3 64.9 1.0
SG B:CYS182 2.3 88.7 1.0
CB B:CYS169 3.2 101.7 1.0
CB B:CYS179 3.3 49.1 1.0
CB B:CYS182 3.4 102.9 1.0
CB B:CYS163 3.5 83.3 1.0
N B:CYS169 3.8 84.9 1.0
CA B:CYS169 4.1 99.6 1.0
CA B:GLY167 4.1 102.2 1.0
N B:CYS182 4.2 65.6 1.0
N B:GLY167 4.2 88.6 1.0
N B:ASN168 4.4 93.8 1.0
CA B:CYS182 4.4 70.4 1.0
CA B:CYS163 4.5 63.0 1.0
C B:GLY167 4.5 85.9 1.0
CB B:ASN165 4.6 66.7 1.0
CA B:CYS179 4.8 69.8 1.0
N B:ASN165 5.0 80.7 1.0
C B:ASN168 5.0 88.2 1.0

Zinc binding site 5 out of 8 in 8hbm

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Zinc binding site 5 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:180.3
occ:1.00
 SG E:CYS155 2.3 125.4 1.0
SG E:CYS135 2.3 239.3 1.0
SG E:CYS138 2.3 162.2 1.0
SG E:CYS152 2.3 161.6 1.0
CB E:CYS135 3.4 234.2 1.0
CB E:CYS155 3.4 122.2 1.0
CB E:CYS138 3.6 179.0 1.0
CB E:CYS152 3.7 151.8 1.0
N E:CYS138 3.8 185.4 1.0
N E:CYS152 4.0 161.9 1.0
N E:CYS155 4.1 124.8 1.0
CA E:CYS138 4.2 181.1 1.0
CA E:CYS155 4.3 119.0 1.0
CB E:ASP140 4.4 161.1 1.0
CA E:CYS152 4.4 151.8 1.0
CB E:ILE137 4.4 163.5 1.0
N E:ASP140 4.7 166.2 1.0
N E:GLY139 4.8 197.2 1.0
C E:ILE137 4.8 169.9 1.0
CA E:CYS135 4.8 232.7 1.0
C E:CYS138 4.8 200.9 1.0
N E:ILE137 4.9 184.4 1.0
CG2 E:ILE137 4.9 163.7 1.0
CA E:ILE137 4.9 180.1 1.0

Zinc binding site 6 out of 8 in 8hbm

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Zinc binding site 6 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:216.1
occ:1.00
 SG E:CYS190 2.3 245.2 1.0
SG E:CYS171 2.3 188.3 1.0
SG E:CYS177 2.3 236.1 1.0
SG E:CYS187 2.3 184.1 1.0
CB E:CYS187 3.1 199.0 1.0
CB E:CYS171 3.3 142.0 1.0
CB E:CYS177 3.4 207.2 1.0
CB E:CYS190 3.5 231.9 1.0
N E:CYS190 4.0 224.5 1.0
CA E:CYS171 4.0 163.0 1.0
N E:CYS177 4.1 227.7 1.0
CA E:LYS175 4.3 174.0 1.0
CA E:CYS190 4.3 203.3 1.0
CA E:CYS177 4.4 223.4 1.0
N E:ARG172 4.6 170.8 1.0
CA E:CYS187 4.6 180.0 1.0
C E:LYS175 4.6 176.1 1.0
N E:ASP176 4.7 211.6 1.0
CB E:TYR189 4.7 222.1 1.0
N E:LYS175 4.7 189.3 1.0
C E:CYS171 4.8 171.4 1.0
CD2 E:TYR189 4.8 242.1 1.0
NH2 E:ARG172 4.9 153.5 1.0

Zinc binding site 7 out of 8 in 8hbm

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Zinc binding site 7 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:136.8
occ:1.00
 SG F:CYS147 2.3 124.4 1.0
SG F:CYS130 2.3 174.3 1.0
SG F:CYS127 2.3 226.0 1.0
SG F:CYS144 2.3 129.8 1.0
CB F:CYS127 3.2 183.2 1.0
CB F:CYS147 3.4 126.9 1.0
CB F:CYS130 3.6 178.1 1.0
NH1 F:ARG176 3.6 180.4 1.0
CB F:CYS144 3.7 154.5 1.0
N F:CYS130 3.9 175.3 1.0
N F:CYS144 4.0 126.8 1.0
N F:CYS147 4.2 122.0 1.0
CA F:CYS130 4.3 175.2 1.0
CB F:ASP132 4.3 195.0 1.0
CA F:CYS144 4.4 114.8 1.0
CA F:CYS147 4.4 126.7 1.0
CB F:VAL129 4.6 178.8 1.0
N F:ASP132 4.6 200.6 1.0
CA F:CYS127 4.7 175.9 1.0
N F:GLY131 4.8 174.4 1.0
CZ F:ARG176 4.8 150.4 1.0
C F:CYS130 4.9 174.7 1.0
C F:VAL129 4.9 176.0 1.0
C F:CYS144 5.0 114.2 1.0
CD F:ARG176 5.0 132.4 1.0
O F:CYS144 5.0 114.6 1.0

Zinc binding site 8 out of 8 in 8hbm

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Zinc binding site 8 out of 8 in the Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:202.8
occ:1.00
 SG F:CYS179 2.3 164.6 1.0
SG F:CYS182 2.3 246.4 1.0
SG F:CYS163 2.3 183.2 1.0
SG F:CYS169 2.3 148.1 1.0
CB F:CYS169 3.2 182.0 1.0
CB F:CYS179 3.3 164.0 1.0
CB F:CYS182 3.5 231.0 1.0
CB F:CYS163 3.5 170.1 1.0
N F:CYS169 3.9 195.5 1.0
N F:GLY167 4.1 242.0 1.0
N F:CYS182 4.2 230.5 1.0
CA F:GLY167 4.2 240.4 1.0
CA F:CYS169 4.2 194.7 1.0
CA F:CYS163 4.3 159.7 1.0
CA F:CYS182 4.4 228.8 1.0
N F:ASN168 4.4 210.6 1.0
CB F:ASN165 4.5 171.4 1.0
C F:GLY167 4.6 241.7 1.0
N F:ASN165 4.6 189.2 1.0
CA F:CYS179 4.8 139.7 1.0
N F:LYS164 4.9 181.9 1.0
CA F:ASN165 5.0 178.3 1.0
C F:CYS163 5.0 168.7 1.0

Reference:

L.Jiang, X.Liu, X.Liang, S.Dai, H.Wei, M.Guo, Z.Chen, D.Xiao, Y.Chen. Structural Basis of the Farnesoid X Receptor/Retinoid X Receptor Heterodimer on Inverted Repeat Dna Comput Struct Biotechnol J V. 21 3149 2023.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2023.05.026
Page generated: Fri Jul 28 07:03:50 2023

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