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Zinc in PDB 3m9e: Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre

Protein crystallography data

The structure of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre, PDB code: 3m9e was solved by Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.18 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.738, 83.468, 75.743, 90.00, 98.28, 90.00
R / Rfree (%) 17.9 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre (pdb code 3m9e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre, PDB code: 3m9e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3m9e

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Zinc binding site 1 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:42.3
occ:1.00
 SG A:CYS123 2.2 41.8 1.0
SG A:CYS126 2.3 46.5 1.0
SG A:CYS109 2.4 50.3 1.0
SG A:CYS106 2.5 59.1 1.0
CB A:CYS109 3.2 37.5 1.0
CB A:CYS126 3.2 52.3 1.0
CB A:CYS106 3.3 34.1 1.0
CB A:CYS123 3.6 43.8 1.0
OD2 A:ASP111 3.7 85.5 1.0
N A:CYS109 3.7 49.5 1.0
N A:CYS126 4.0 38.8 1.0
N A:CYS123 4.0 38.3 1.0
CA A:CYS109 4.0 50.0 1.0
NH1 A:ARG157 4.2 47.7 1.0
CA A:CYS126 4.2 43.4 1.0
CA A:CYS123 4.3 40.8 1.0
CB A:VAL108 4.4 47.2 1.0
N A:GLY110 4.6 49.6 1.0
C A:CYS109 4.7 49.2 1.0
C A:VAL108 4.7 48.2 1.0
CD A:ARG157 4.7 48.9 1.0
CA A:CYS106 4.8 53.0 1.0
CG1 A:VAL108 4.8 37.6 1.0
NH1 A:ARG164 4.9 27.9 1.0
O A:CYS123 4.9 39.7 1.0
C A:CYS123 4.9 42.3 1.0
CA A:VAL108 5.0 46.2 1.0
CG A:ASP111 5.0 74.1 1.0

Zinc binding site 2 out of 8 in 3m9e

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Zinc binding site 2 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:44.8
occ:1.00
 SG A:CYS144 2.0 47.2 1.0
SG A:CYS150 2.3 42.2 1.0
SG A:CYS160 2.4 37.1 1.0
SG A:CYS163 2.5 46.3 1.0
CB A:CYS144 3.0 32.0 1.0
CB A:CYS150 3.2 39.3 1.0
CB A:CYS163 3.3 32.4 1.0
CB A:CYS160 3.4 32.2 1.0
O A:GLU147 3.8 75.8 1.0
CA A:CYS144 3.9 44.9 1.0
N A:CYS150 4.1 49.6 1.0
O A:HOH213 4.1 63.1 1.0
O A:HOH29 4.2 34.4 1.0
N A:CYS163 4.2 37.8 1.0
CA A:CYS150 4.3 47.1 1.0
CA A:CYS163 4.4 36.5 1.0
CA A:GLY148 4.5 40.3 1.0
C A:CYS144 4.7 53.3 1.0
C A:GLU147 4.8 73.2 1.0
O A:TYR146 4.8 54.5 1.0
N A:LYS149 4.8 52.7 1.0
C A:GLY148 4.8 49.1 1.0
CA A:CYS160 4.8 31.6 1.0
N A:LYS145 5.0 51.6 1.0
CD2 A:TYR146 5.0 41.9 1.0

Zinc binding site 3 out of 8 in 3m9e

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Zinc binding site 3 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn208

b:40.8
occ:1.00
 SG B:CYS123 2.2 38.0 1.0
SG B:CYS109 2.3 35.5 1.0
SG B:CYS126 2.3 32.4 1.0
SG B:CYS106 2.4 41.0 1.0
CB B:CYS109 3.2 27.4 1.0
CB B:CYS106 3.3 47.0 1.0
CB B:CYS126 3.4 38.5 1.0
CB B:CYS123 3.6 43.1 1.0
N B:CYS109 3.7 30.7 1.0
OD2 B:ASP111 3.7 67.6 1.0
CA B:CYS109 4.0 35.7 1.0
N B:CYS123 4.1 41.0 1.0
N B:CYS126 4.2 27.0 1.0
NH1 B:ARG157 4.2 50.0 1.0
CB B:VAL108 4.3 31.0 1.0
CA B:CYS126 4.4 28.6 1.0
CA B:CYS123 4.4 41.8 1.0
N B:GLY110 4.5 48.5 1.0
C B:CYS109 4.6 45.5 1.0
C B:VAL108 4.6 38.1 1.0
CG1 B:VAL108 4.7 32.2 1.0
CA B:CYS106 4.8 45.6 1.0
NH1 B:ARG164 4.8 27.6 1.0
CA B:VAL108 4.9 37.9 1.0
CD B:ARG157 4.9 38.3 1.0
CG B:ASP111 4.9 59.5 1.0
N B:VAL108 5.0 39.5 1.0

Zinc binding site 4 out of 8 in 3m9e

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Zinc binding site 4 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn209

b:40.7
occ:1.00
 SG B:CYS150 2.2 33.0 1.0
SG B:CYS160 2.3 31.6 1.0
SG B:CYS144 2.3 38.5 1.0
SG B:CYS163 2.5 37.9 1.0
CB B:CYS150 3.2 42.1 1.0
CB B:CYS160 3.2 14.7 1.0
CB B:CYS163 3.2 26.4 1.0
CB B:CYS144 3.3 26.1 1.0
N B:CYS150 4.0 37.2 1.0
O B:GLU147 4.0 82.4 1.0
O B:HOH10 4.0 27.2 1.0
CA B:CYS144 4.1 34.7 1.0
CA B:CYS150 4.2 37.7 1.0
N B:CYS163 4.2 30.6 1.0
CA B:CYS163 4.3 34.5 1.0
CA B:GLY148 4.5 54.1 1.0
N B:LYS149 4.6 40.3 1.0
O B:HOH2 4.6 39.8 1.0
CA B:CYS160 4.7 26.2 1.0
CD2 B:TYR146 4.8 42.1 1.0
C B:GLY148 4.8 48.5 1.0
O B:TYR146 4.8 61.0 1.0
C B:GLU147 4.9 74.0 1.0
C B:CYS144 4.9 38.4 1.0
N B:LYS145 4.9 42.2 1.0

Zinc binding site 5 out of 8 in 3m9e

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Zinc binding site 5 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn208

b:40.9
occ:1.00
 SG E:CYS123 2.2 37.4 1.0
SG E:CYS109 2.3 40.0 1.0
SG E:CYS126 2.4 38.4 1.0
SG E:CYS106 2.4 38.6 1.0
CB E:CYS106 3.2 40.6 1.0
CB E:CYS126 3.3 38.9 1.0
CB E:CYS109 3.3 44.5 1.0
CB E:CYS123 3.6 30.5 1.0
N E:CYS109 3.7 29.7 1.0
N E:CYS123 3.9 36.3 1.0
OD2 E:ASP111 4.0 76.6 1.0
NH1 E:ARG157 4.0 52.9 1.0
CA E:CYS109 4.1 40.8 1.0
N E:CYS126 4.2 34.1 1.0
CB E:VAL108 4.3 35.6 1.0
CA E:CYS123 4.3 33.1 1.0
CA E:CYS126 4.3 37.0 1.0
N E:GLY110 4.6 41.2 1.0
C E:CYS109 4.7 44.8 1.0
CA E:CYS106 4.7 46.9 1.0
C E:VAL108 4.7 35.6 1.0
CG1 E:VAL108 4.8 27.1 1.0
CA E:VAL108 4.9 38.8 1.0
NH1 E:ARG164 4.9 35.2 1.0
N E:VAL108 4.9 43.5 1.0
C E:THR122 5.0 41.8 1.0

Zinc binding site 6 out of 8 in 3m9e

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Zinc binding site 6 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn209

b:40.6
occ:1.00
 SG E:CYS150 2.2 38.1 1.0
SG E:CYS160 2.4 32.8 1.0
SG E:CYS144 2.4 43.6 1.0
SG E:CYS163 2.5 46.7 1.0
CB E:CYS150 3.1 38.0 1.0
CB E:CYS160 3.2 23.2 1.0
CB E:CYS144 3.3 22.5 1.0
CB E:CYS163 3.4 24.0 1.0
O E:GLU147 3.9 72.5 1.0
O E:HOH211 4.0 38.4 1.0
CA E:CYS144 4.0 36.2 1.0
N E:CYS150 4.1 37.5 1.0
CA E:CYS150 4.2 37.9 1.0
N E:CYS163 4.2 31.2 1.0
CA E:CYS163 4.4 33.2 1.0
CA E:GLY148 4.5 52.5 1.0
CA E:CYS160 4.7 32.5 1.0
O E:HOH71 4.7 38.2 1.0
O E:TYR146 4.8 57.5 1.0
N E:LYS149 4.8 46.2 1.0
C E:GLU147 4.8 70.5 1.0
C E:GLY148 4.8 50.6 1.0
C E:CYS144 4.8 46.1 1.0
N E:LYS145 4.9 48.4 1.0
CD2 E:TYR146 4.9 45.6 1.0

Zinc binding site 7 out of 8 in 3m9e

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Zinc binding site 7 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn208

b:41.0
occ:1.00
 SG F:CYS123 2.3 38.8 1.0
SG F:CYS109 2.3 50.6 1.0
SG F:CYS126 2.4 38.0 1.0
SG F:CYS106 2.4 45.1 1.0
CB F:CYS109 3.2 40.6 1.0
CB F:CYS106 3.3 44.3 1.0
CB F:CYS126 3.5 41.2 1.0
OD2 F:ASP111 3.6 75.0 1.0
CB F:CYS123 3.7 53.2 1.0
N F:CYS109 3.8 39.4 1.0
NH1 F:ARG157 4.0 44.1 1.0
CA F:CYS109 4.0 41.7 1.0
N F:CYS123 4.0 40.4 1.0
N F:CYS126 4.1 39.2 1.0
CB F:VAL108 4.4 38.3 1.0
CA F:CYS126 4.4 35.6 1.0
CA F:CYS123 4.4 43.3 1.0
C F:CYS109 4.6 46.8 1.0
N F:GLY110 4.6 51.5 1.0
C F:VAL108 4.7 44.8 1.0
CA F:CYS106 4.7 48.7 1.0
CG F:ASP111 4.8 68.8 1.0
NH1 F:ARG164 4.9 25.0 1.0
CA F:VAL108 5.0 44.2 1.0

Zinc binding site 8 out of 8 in 3m9e

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Zinc binding site 8 out of 8 in the Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Thyroid Hormone Beta Dna Binding Domain Homodimer with Inverted Palindrome Tre within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn209

b:43.7
occ:1.00
 SG F:CYS150 2.3 44.2 1.0
SG F:CYS144 2.3 43.2 1.0
SG F:CYS160 2.4 37.5 1.0
SG F:CYS163 2.4 50.5 1.0
CB F:CYS150 3.1 36.1 1.0
CB F:CYS160 3.2 25.1 1.0
CB F:CYS144 3.2 30.1 1.0
CB F:CYS163 3.3 39.4 1.0
O F:HOH46 3.8 35.8 1.0
O F:GLU147 3.9 77.4 1.0
CA F:CYS144 4.0 45.1 1.0
N F:CYS150 4.0 44.2 1.0
CA F:CYS150 4.2 41.8 1.0
N F:CYS163 4.2 31.5 1.0
CA F:CYS163 4.3 40.8 1.0
O F:HOH223 4.4 75.1 1.0
CA F:GLY148 4.4 54.7 1.0
CA F:CYS160 4.6 37.0 1.0
N F:LYS149 4.7 48.2 1.0
C F:GLY148 4.7 48.0 1.0
C F:CYS144 4.8 48.2 1.0
C F:GLU147 4.8 75.7 1.0
N F:LYS145 4.9 48.4 1.0
CD2 F:TYR146 4.9 37.5 1.0

Reference:

Y.Chen, M.A.Young. Structure of A Thyroid Hormone Receptor Dna-Binding Domain Homodimer Bound to An Inverted Palindrome Dna Response Element. Mol.Endocrinol. V. 24 1650 2010.
ISSN: ISSN 0888-8809
PubMed: 20610536
DOI: 10.1210/ME.2010-0129
Page generated: Wed Dec 16 04:34:39 2020

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