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Zinc in PDB 8j54: Crystal Structure of Rxr/DR2 Complex

Protein crystallography data

The structure of Crystal Structure of Rxr/DR2 Complex, PDB code: 8j54 was solved by Y.Chen, L.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.79 / 2.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.239, 63.646, 244.649, 90, 90, 90
R / Rfree (%) 21.7 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rxr/DR2 Complex (pdb code 8j54). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Rxr/DR2 Complex, PDB code: 8j54:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8j54

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Zinc binding site 1 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:120.3
occ:1.00
 SG C:CYS194 2.3 136.9 1.0
SG C:CYS191 2.3 118.7 1.0
SG C:CYS181 2.3 133.1 1.0
SG C:CYS175 2.3 128.3 1.0
CB C:CYS191 3.3 114.5 1.0
CB C:CYS175 3.4 115.9 1.0
CB C:CYS194 3.5 120.0 1.0
CB C:CYS181 3.5 132.6 1.0
N C:CYS181 4.0 135.3 1.0
N C:CYS194 4.1 116.0 1.0
CA C:CYS175 4.3 118.3 1.0
CA C:LYS179 4.3 126.7 1.0
N C:ASP180 4.4 135.5 1.0
CB C:ASP177 4.4 134.8 1.0
CA C:CYS194 4.4 116.3 1.0
CA C:CYS181 4.4 138.3 1.0
N C:LYS179 4.4 141.1 1.0
CD1 C:TYR193 4.7 109.1 1.0
C C:LYS179 4.7 124.3 1.0
CA C:CYS191 4.8 118.5 1.0
CB C:TYR193 4.9 102.2 1.0
N C:ASP177 5.0 129.7 1.0
C C:CYS175 5.0 122.4 1.0

Zinc binding site 2 out of 8 in 8j54

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Zinc binding site 2 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:89.1
occ:1.00
 SG C:CYS159 2.3 101.1 1.0
SG C:CYS142 2.3 111.4 1.0
SG C:CYS156 2.3 91.0 1.0
SG C:CYS139 2.3 105.8 1.0
CB C:CYS159 3.3 97.8 1.0
CB C:CYS142 3.4 91.2 1.0
CB C:CYS139 3.5 101.7 1.0
CB C:CYS156 3.6 89.3 1.0
N C:CYS142 3.8 115.5 1.0
N C:CYS156 4.0 87.1 1.0
NH1 C:ARG188 4.0 95.2 1.0
NH2 C:ARG195 4.1 98.6 1.0
N C:CYS159 4.1 80.3 1.0
CA C:CYS142 4.2 103.7 1.0
CA C:CYS159 4.3 88.3 1.0
CA C:CYS156 4.4 93.9 1.0
CB C:ASP144 4.5 106.8 1.0
CB C:ILE141 4.5 100.7 1.0
C C:CYS142 4.7 103.2 1.0
CG2 C:ILE141 4.7 90.1 1.0
N C:ASP144 4.8 110.8 1.0
C C:ILE141 4.8 112.7 1.0
N C:GLY143 4.9 113.1 1.0
CA C:CYS139 4.9 96.4 1.0
CD C:ARG188 5.0 104.4 1.0

Zinc binding site 3 out of 8 in 8j54

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Zinc binding site 3 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:89.4
occ:1.00
 SG D:CYS156 2.3 73.9 1.0
SG D:CYS159 2.3 99.3 1.0
SG D:CYS142 2.3 98.7 1.0
SG D:CYS139 2.3 106.7 1.0
CB D:CYS159 3.4 96.7 1.0
CB D:CYS139 3.4 100.4 1.0
CB D:CYS142 3.6 98.2 1.0
CB D:CYS156 3.7 112.2 1.0
N D:CYS142 3.9 94.9 1.0
N D:CYS156 4.0 98.6 1.0
NH1 D:ARG188 4.1 72.9 1.0
N D:CYS159 4.2 79.6 1.0
CA D:CYS142 4.2 103.1 1.0
CA D:CYS159 4.4 84.5 1.0
CB D:ASP144 4.4 98.4 1.0
CA D:CYS156 4.5 113.0 1.0
CB D:ILE141 4.5 102.9 1.0
CG2 D:ILE141 4.5 95.3 1.0
C D:CYS142 4.8 100.1 1.0
N D:ASP144 4.8 96.8 1.0
C D:ILE141 4.8 101.9 1.0
CA D:CYS139 4.9 105.6 1.0

Zinc binding site 4 out of 8 in 8j54

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Zinc binding site 4 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:122.8
occ:1.00
 SG D:CYS175 2.3 116.5 1.0
SG D:CYS181 2.3 142.8 1.0
SG D:CYS191 2.3 132.0 1.0
CB D:CYS191 3.1 106.9 1.0
SG D:CYS194 3.5 125.3 1.0
OD2 D:ASP177 3.7 139.8 1.0
CB D:CYS175 3.7 113.6 1.0
CB D:CYS181 3.9 148.8 1.0
CG D:ASP177 4.1 139.5 1.0
CB D:ASP177 4.1 141.8 1.0
OE1 C:GLU211 4.2 127.3 1.0
N D:ASP177 4.2 139.7 1.0
CA D:CYS175 4.3 117.9 1.0
N D:ARG176 4.3 116.1 1.0
CA D:CYS191 4.5 116.9 1.0
CB D:CYS194 4.7 126.6 1.0
CA D:ASP177 4.7 144.0 1.0
N D:CYS181 4.8 142.4 1.0
C D:CYS175 4.8 123.1 1.0
N D:LYS179 4.8 144.4 1.0
CA D:LYS179 4.8 137.9 1.0
CA D:CYS181 4.9 143.0 1.0
OD1 D:ASP177 5.0 145.1 1.0

Zinc binding site 5 out of 8 in 8j54

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Zinc binding site 5 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:76.7
occ:1.00
 SG E:CYS159 2.3 87.4 1.0
SG E:CYS156 2.3 85.5 1.0
SG E:CYS139 2.3 109.0 1.0
SG E:CYS142 2.3 82.4 1.0
CB E:CYS159 3.3 78.8 1.0
CB E:CYS139 3.5 93.8 1.0
CB E:CYS142 3.5 91.8 1.0
CB E:CYS156 3.6 85.5 1.0
N E:CYS142 3.9 104.3 1.0
N E:CYS156 3.9 80.8 1.0
N E:CYS159 4.1 64.3 1.0
NH1 E:ARG188 4.1 102.2 1.0
CA E:CYS142 4.2 100.9 1.0
CA E:CYS156 4.3 86.5 1.0
CA E:CYS159 4.3 66.8 1.0
CB E:ASP144 4.4 102.6 1.0
CB E:ILE141 4.4 99.9 1.0
OG E:SER155 4.6 93.4 1.0
CG2 E:ILE141 4.6 103.1 1.0
C E:CYS142 4.8 100.9 1.0
C E:ILE141 4.8 105.7 1.0
N E:ASP144 4.9 110.1 1.0
C E:CYS156 4.9 79.0 1.0
CA E:CYS139 4.9 101.1 1.0
O E:CYS156 4.9 77.7 1.0
N E:ILE141 5.0 93.8 1.0
CA E:ILE141 5.0 97.1 1.0

Zinc binding site 6 out of 8 in 8j54

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Zinc binding site 6 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:101.0
occ:1.00
 SG E:CYS191 2.3 104.3 1.0
SG E:CYS181 2.3 117.3 1.0
SG E:CYS194 2.3 131.6 1.0
SG E:CYS175 2.3 145.7 1.0
CB E:CYS191 3.3 95.9 1.0
CB E:CYS194 3.5 94.2 1.0
CB E:CYS181 3.5 136.4 1.0
CB E:CYS175 3.6 128.9 1.0
CA E:LYS179 4.0 143.3 1.0
N E:CYS194 4.1 91.2 1.0
N E:CYS181 4.1 134.0 1.0
CA E:CYS194 4.4 91.2 1.0
C E:LYS179 4.4 146.0 1.0
CA E:CYS181 4.4 131.1 1.0
N E:LYS179 4.5 138.9 1.0
N E:ASP180 4.5 149.0 1.0
CA E:CYS175 4.5 131.7 1.0
OD2 E:ASP177 4.6 138.5 1.0
CD2 E:TYR193 4.6 114.4 1.0
CA E:CYS191 4.7 93.1 1.0
CB E:TYR193 4.9 103.9 1.0

Zinc binding site 7 out of 8 in 8j54

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Zinc binding site 7 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:85.2
occ:1.00
 SG F:CYS142 2.3 109.6 1.0
SG F:CYS159 2.3 88.5 1.0
SG F:CYS156 2.3 84.3 1.0
SG F:CYS139 2.3 99.4 1.0
CB F:CYS159 3.3 77.0 1.0
CB F:CYS139 3.4 98.5 1.0
CB F:CYS142 3.6 97.4 1.0
CB F:CYS156 3.6 88.6 1.0
N F:CYS142 3.9 113.3 1.0
N F:CYS156 3.9 83.3 1.0
NH1 F:ARG188 4.0 87.8 1.0
N F:CYS159 4.1 65.9 1.0
CA F:CYS142 4.3 98.3 1.0
CA F:CYS156 4.3 88.1 1.0
CA F:CYS159 4.3 73.6 1.0
CB F:ASP144 4.5 97.8 1.0
CB F:ILE141 4.6 102.2 1.0
CG2 F:ILE141 4.7 98.8 1.0
C F:CYS142 4.8 104.8 1.0
CA F:CYS139 4.9 98.0 1.0
N F:ASP144 4.9 94.7 1.0
C F:ILE141 4.9 108.6 1.0
CD F:ARG188 4.9 105.0 1.0
C F:CYS156 4.9 79.4 1.0
O F:CYS156 5.0 80.6 1.0

Zinc binding site 8 out of 8 in 8j54

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Zinc binding site 8 out of 8 in the Crystal Structure of Rxr/DR2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Rxr/DR2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:115.2
occ:1.00
 SG F:CYS181 2.3 120.5 1.0
SG F:CYS191 2.3 111.0 1.0
SG F:CYS194 2.3 125.4 1.0
SG F:CYS175 2.3 130.6 1.0
CB F:CYS181 3.4 124.2 1.0
CB F:CYS194 3.4 99.0 1.0
CB F:CYS191 3.5 110.1 1.0
CB F:CYS175 3.6 120.9 1.0
N F:CYS181 4.0 125.8 1.0
N F:CYS194 4.1 96.0 1.0
CA F:CYS181 4.3 124.1 1.0
CA F:CYS194 4.4 97.0 1.0
CA F:CYS175 4.4 127.1 1.0
CA F:LYS179 4.4 129.7 1.0
N F:ASP180 4.5 148.0 1.0
N F:LYS179 4.6 151.2 1.0
CD2 F:TYR193 4.6 104.3 1.0
CB F:ASP177 4.7 165.3 1.0
CB F:TYR193 4.9 105.5 1.0
CA F:CYS191 4.9 125.2 1.0
C F:LYS179 4.9 138.7 1.0

Reference:

Y.Chen, L.Jiang. Structural Characterization of the Dna Binding Mechanism of Retinoic Acid-Related Orphan Receptor Gamma Structure 2024.
ISSN: ISSN 0969-2126
Page generated: Thu Oct 31 08:04:21 2024

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