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Zinc in PDB 4oor: Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element

Protein crystallography data

The structure of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element, PDB code: 4oor was solved by E.O.Ortlund, M.N.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.58 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.472, 80.374, 115.645, 90.00, 96.74, 90.00
R / Rfree (%) 19.1 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element (pdb code 4oor). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element, PDB code: 4oor:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4oor

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Zinc binding site 1 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:41.4
occ:1.00
SG A:CYS59 2.2 26.9 1.0
SG A:CYS43 2.3 45.1 1.0
SG A:CYS49 2.3 39.5 1.0
SG A:CYS62 2.3 33.3 1.0
CB A:CYS49 3.3 27.5 1.0
CB A:CYS43 3.3 17.6 1.0
CB A:CYS59 3.3 23.8 1.0
O A:HOH201 3.4 32.6 1.0
CB A:CYS62 3.6 29.7 1.0
CA A:CYS43 3.9 33.2 1.0
N A:CYS49 4.1 26.5 1.0
CA A:CYS49 4.3 22.5 1.0
N A:CYS62 4.3 23.9 1.0
CA A:ASN47 4.5 37.6 1.0
CA A:CYS62 4.5 35.8 1.0
N A:ALA44 4.5 35.5 1.0
N A:ASN47 4.6 32.1 1.0
C A:CYS43 4.7 39.3 1.0
N A:GLY45 4.7 23.9 1.0
CA A:CYS59 4.7 32.0 1.0
N A:ASP48 4.8 29.9 1.0
O A:HOH207 4.8 36.8 1.0
C A:ASN47 4.9 36.2 1.0

Zinc binding site 2 out of 8 in 4oor

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Zinc binding site 2 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:43.3
occ:1.00
SG A:CYS10 2.2 41.0 1.0
SG A:CYS27 2.3 36.0 1.0
SG A:CYS7 2.3 37.4 1.0
SG A:CYS24 2.4 47.2 1.0
CB A:CYS27 3.3 28.6 1.0
CB A:CYS7 3.4 42.9 1.0
CB A:CYS10 3.6 27.6 1.0
CB A:CYS24 3.8 47.0 1.0
N A:CYS10 3.9 32.3 1.0
NH1 A:ARG56 4.0 50.1 1.0
N A:CYS24 4.1 36.7 1.0
OG A:SER26 4.2 65.3 1.0
N A:CYS27 4.3 30.7 1.0
CA A:CYS10 4.3 36.8 1.0
CB A:ILE9 4.3 33.1 1.0
CA A:CYS27 4.4 36.7 1.0
CA A:CYS24 4.5 41.8 1.0
CB A:ASP12 4.7 48.3 1.0
C A:ILE9 4.7 30.4 1.0
CA A:CYS7 4.8 36.6 1.0
NH2 A:ARG63 4.9 29.8 1.0
CA A:ILE9 4.9 29.6 1.0
C A:CYS10 5.0 43.7 1.0
N A:ILE9 5.0 23.5 1.0
N A:GLY11 5.0 43.3 1.0

Zinc binding site 3 out of 8 in 4oor

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Zinc binding site 3 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:44.5
occ:1.00
SG B:CYS27 2.3 42.3 1.0
SG B:CYS10 2.3 45.5 1.0
SG B:CYS24 2.4 50.3 1.0
SG B:CYS7 2.4 49.9 1.0
CB B:CYS27 3.2 35.7 1.0
CB B:CYS7 3.4 52.9 1.0
CB B:CYS10 3.7 36.2 1.0
CB B:CYS24 3.8 62.3 1.0
N B:CYS10 3.9 43.1 1.0
N B:CYS24 4.1 48.0 1.0
NH1 B:ARG56 4.1 46.4 1.0
OG B:SER26 4.1 65.0 1.0
N B:CYS27 4.3 34.9 1.0
CB B:ILE9 4.3 35.3 1.0
CA B:CYS27 4.4 39.3 1.0
CA B:CYS10 4.4 43.9 1.0
CA B:CYS24 4.5 48.7 1.0
CB B:ASP12 4.6 44.0 1.0
NH2 B:ARG63 4.7 28.3 1.0
C B:ILE9 4.8 44.8 1.0
CA B:CYS7 4.9 49.4 1.0
CA B:ILE9 5.0 39.9 1.0
N B:ASP12 5.0 37.8 1.0

Zinc binding site 4 out of 8 in 4oor

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Zinc binding site 4 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:37.4
occ:1.00
SG B:CYS59 2.2 29.8 1.0
SG B:CYS49 2.3 37.3 1.0
SG B:CYS62 2.3 35.7 1.0
SG B:CYS43 2.4 26.6 1.0
CB B:CYS59 3.2 16.5 1.0
CB B:CYS49 3.3 23.5 1.0
CB B:CYS43 3.4 32.3 1.0
CB B:CYS62 3.5 19.8 1.0
O B:HOH201 3.7 23.1 1.0
CA B:CYS43 4.0 34.0 1.0
N B:CYS62 4.3 20.9 1.0
N B:CYS49 4.4 26.9 1.0
CA B:CYS49 4.5 33.2 1.0
CA B:CYS62 4.5 26.6 1.0
N B:ALA44 4.5 33.0 1.0
CA B:ASN47 4.6 49.2 1.0
N B:ASN47 4.6 48.3 1.0
N B:GLY45 4.6 35.7 1.0
CA B:CYS59 4.6 29.5 1.0
C B:CYS43 4.7 41.1 1.0
O B:CYS59 4.9 42.9 1.0

Zinc binding site 5 out of 8 in 4oor

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Zinc binding site 5 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:35.6
occ:1.00
SG E:CYS59 2.2 26.2 1.0
SG E:CYS49 2.3 38.0 1.0
SG E:CYS62 2.3 28.8 1.0
SG E:CYS43 2.3 33.1 1.0
CB E:CYS49 3.2 31.9 1.0
CB E:CYS59 3.3 16.8 1.0
CB E:CYS43 3.3 34.4 1.0
CB E:CYS62 3.5 28.3 1.0
O E:HOH201 3.6 32.3 1.0
CA E:CYS43 3.9 34.5 1.0
N E:CYS49 4.0 28.4 1.0
CA E:CYS49 4.2 36.7 1.0
N E:CYS62 4.4 32.8 1.0
O E:HOH202 4.4 29.2 1.0
CA E:ASN47 4.5 29.6 1.0
CA E:CYS62 4.5 31.9 1.0
N E:ASN47 4.6 27.9 1.0
N E:ALA44 4.6 41.4 1.0
N E:ASP48 4.7 32.0 1.0
CA E:CYS59 4.7 29.5 1.0
C E:CYS43 4.7 37.8 1.0
C E:ASN47 4.8 32.1 1.0
N E:GLY45 4.8 26.8 1.0

Zinc binding site 6 out of 8 in 4oor

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Zinc binding site 6 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:38.0
occ:1.00
SG E:CYS10 2.2 35.2 1.0
SG E:CYS7 2.4 47.2 1.0
SG E:CYS24 2.4 36.1 1.0
SG E:CYS27 2.4 44.5 1.0
CB E:CYS27 3.4 28.2 1.0
CB E:CYS7 3.4 46.4 1.0
CB E:CYS10 3.5 35.0 1.0
N E:CYS10 3.6 40.1 1.0
CB E:CYS24 3.7 43.6 1.0
N E:CYS24 4.0 35.2 1.0
CB E:ILE9 4.1 42.3 1.0
CA E:CYS10 4.1 36.6 1.0
NH1 E:ARG56 4.4 45.1 1.0
CA E:CYS24 4.4 35.0 1.0
OG E:SER26 4.5 47.2 1.0
N E:CYS27 4.5 39.8 1.0
C E:ILE9 4.5 37.4 1.0
CB E:ASP12 4.5 37.2 1.0
CA E:CYS27 4.6 40.9 1.0
CA E:ILE9 4.7 40.5 1.0
C E:CYS10 4.8 39.2 1.0
N E:ILE9 4.8 36.4 1.0
CG2 E:ILE9 4.8 26.0 1.0
N E:GLY11 4.8 42.0 1.0
N E:ASP12 4.9 24.8 1.0
CA E:CYS7 4.9 40.0 1.0
CG1 E:ILE9 4.9 41.0 1.0
NH2 E:ARG63 5.0 39.6 1.0

Zinc binding site 7 out of 8 in 4oor

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Zinc binding site 7 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:33.9
occ:1.00
SG F:CYS59 2.2 28.2 1.0
SG F:CYS62 2.3 30.2 1.0
SG F:CYS49 2.3 36.8 1.0
SG F:CYS43 2.4 27.5 1.0
CB F:CYS49 3.2 26.4 1.0
CB F:CYS59 3.4 31.8 1.0
CB F:CYS43 3.4 21.0 1.0
CB F:CYS62 3.5 27.2 1.0
O F:HOH203 3.7 24.4 1.0
CA F:CYS43 4.0 24.2 1.0
N F:CYS49 4.2 25.9 1.0
N F:CYS62 4.2 14.1 1.0
CA F:CYS49 4.3 30.9 1.0
CA F:CYS62 4.5 26.9 1.0
O F:HOH206 4.5 36.0 1.0
CA F:ASN47 4.6 40.4 1.0
N F:ASN47 4.6 35.8 1.0
N F:ALA44 4.6 25.8 1.0
N F:GLY45 4.7 36.9 1.0
CA F:CYS59 4.7 24.1 1.0
C F:CYS43 4.8 26.0 1.0
N F:ASP48 4.8 41.0 1.0
O F:HOH201 4.9 24.0 1.0
O F:CYS59 4.9 22.8 1.0
C F:ASN47 5.0 43.3 1.0

Zinc binding site 8 out of 8 in 4oor

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Zinc binding site 8 out of 8 in the Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ancestral Steroid Receptor 2 Dna Binding Domain in Complex with A Steroid Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn102

b:44.2
occ:1.00
SG F:CYS10 2.2 31.7 1.0
SG F:CYS27 2.3 34.7 1.0
SG F:CYS24 2.3 43.5 1.0
SG F:CYS7 2.4 41.5 1.0
CB F:CYS7 3.3 44.5 1.0
CB F:CYS27 3.3 24.0 1.0
CB F:CYS10 3.6 25.4 1.0
CB F:CYS24 3.8 37.0 1.0
N F:CYS10 4.0 31.7 1.0
N F:CYS24 4.1 27.9 1.0
OG F:SER26 4.1 48.1 1.0
N F:CYS27 4.3 21.8 1.0
NH1 F:ARG56 4.3 45.4 1.0
CA F:CYS10 4.4 24.5 1.0
CA F:CYS27 4.4 30.0 1.0
CB F:ILE9 4.4 43.2 1.0
CA F:CYS24 4.5 35.1 1.0
CB F:ASP12 4.6 56.6 1.0
CA F:CYS7 4.8 34.6 1.0
C F:ILE9 4.9 36.4 1.0
NH2 F:ARG63 4.9 41.2 1.0
N F:ASP12 5.0 41.6 1.0
C F:CYS10 5.0 33.4 1.0

Reference:

A.N.Mckeown, J.T.Bridgham, D.W.Anderson, M.N.Murphy, E.A.Ortlund, J.W.Thornton. Evolution of Dna Specificity in A Transcription Factor Family Produced A New Gene Regulatory Module. Cell(Cambridge,Mass.) V. 159 58 2014.
ISSN: ISSN 0092-8674
PubMed: 25259920
DOI: 10.1016/J.CELL.2014.09.003
Page generated: Wed Dec 16 05:39:20 2020

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