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Zinc in PDB 4ond: Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex

Protein crystallography data

The structure of Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex, PDB code: 4ond 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) 37.56 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.272, 79.829, 116.782, 90.00, 96.75, 90.00
R / Rfree (%) 18.6 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex (pdb code 4ond). 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 Dbd Helix Mutant - Ere Dna Complex, PDB code: 4ond:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4ond

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Zinc binding site 1 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:39.3
occ:1.00
 SG A:CYS59 2.3 32.2 1.0
SG A:CYS43 2.3 35.3 1.0
SG A:CYS62 2.4 36.6 1.0
SG A:CYS49 2.5 42.5 1.0
CB A:CYS49 3.4 40.3 1.0
CB A:CYS43 3.4 34.5 1.0
CB A:CYS59 3.4 31.5 1.0
CB A:CYS62 3.5 31.4 1.0
O A:HOH206 3.9 42.6 1.0
CA A:CYS43 4.0 37.2 1.0
O A:HOH201 4.2 43.3 1.0
N A:CYS49 4.2 37.7 1.0
N A:CYS62 4.3 32.2 1.0
CA A:CYS49 4.4 41.9 1.0
CA A:CYS62 4.5 34.3 1.0
CA A:ASN47 4.5 40.4 1.0
N A:ASN47 4.6 35.9 1.0
N A:ALA44 4.7 31.5 1.0
N A:ASP48 4.8 39.2 1.0
N A:GLY45 4.8 43.9 1.0
C A:CYS43 4.8 34.0 1.0
CA A:CYS59 4.8 36.8 1.0
O A:HOH208 4.9 40.0 1.0
C A:ASN47 5.0 44.6 1.0

Zinc binding site 2 out of 8 in 4ond

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Zinc binding site 2 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:42.5
occ:1.00
 SG A:CYS10 2.2 41.0 1.0
SG A:CYS24 2.3 41.9 1.0
SG A:CYS7 2.3 41.1 1.0
SG A:CYS27 2.3 42.4 1.0
CB A:CYS27 3.3 40.2 1.0
CB A:CYS7 3.3 48.2 1.0
CB A:CYS10 3.4 41.2 1.0
CB A:CYS24 3.6 37.0 1.0
N A:CYS10 3.7 40.9 1.0
N A:CYS24 3.9 43.9 1.0
NH1 A:ARG56 4.0 47.9 1.0
CA A:CYS10 4.1 39.9 1.0
N A:CYS27 4.2 38.6 1.0
CA A:CYS24 4.3 39.4 1.0
CA A:CYS27 4.4 38.6 1.0
CB A:ILE9 4.5 49.7 1.0
C A:ILE9 4.7 46.0 1.0
CA A:CYS7 4.8 45.3 1.0
C A:CYS10 4.8 50.5 1.0
N A:GLY11 4.9 48.5 1.0
CG2 A:ILE9 4.9 40.1 1.0
CA A:ILE9 4.9 47.8 1.0
N A:ILE9 5.0 35.7 1.0
NH2 A:ARG63 5.0 36.4 1.0
C A:CYS24 5.0 39.3 1.0
C A:THR23 5.0 46.8 1.0

Zinc binding site 3 out of 8 in 4ond

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Zinc binding site 3 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:41.8
occ:1.00
 SG B:CYS10 2.2 39.7 1.0
SG B:CYS24 2.3 41.7 1.0
SG B:CYS27 2.3 39.5 1.0
SG B:CYS7 2.4 38.6 1.0
CB B:CYS27 3.3 38.9 1.0
CB B:CYS7 3.3 49.1 1.0
CB B:CYS10 3.4 38.8 1.0
CB B:CYS24 3.6 37.8 1.0
N B:CYS10 3.7 38.2 1.0
NH1 B:ARG56 3.9 56.8 1.0
N B:CYS24 3.9 39.7 1.0
CA B:CYS10 4.1 44.2 1.0
CB B:ILE9 4.2 38.9 1.0
N B:CYS27 4.2 31.6 1.0
CA B:CYS24 4.3 37.8 1.0
CA B:CYS27 4.4 38.5 1.0
C B:ILE9 4.6 48.2 1.0
CB B:ASP12 4.6 54.0 1.0
CA B:CYS7 4.8 43.8 1.0
C B:CYS10 4.8 50.2 1.0
CA B:ILE9 4.8 46.8 1.0
N B:GLY11 4.9 44.3 1.0
CG2 B:ILE9 4.9 40.4 1.0
N B:ILE9 4.9 43.3 1.0
N B:ASP12 4.9 50.2 1.0
NH2 B:ARG63 4.9 32.0 1.0
C B:CYS24 5.0 41.5 1.0

Zinc binding site 4 out of 8 in 4ond

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Zinc binding site 4 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:39.5
occ:1.00
 SG B:CYS59 2.2 35.1 1.0
SG B:CYS62 2.4 36.8 1.0
SG B:CYS43 2.4 39.5 1.0
SG B:CYS49 2.4 38.9 1.0
CB B:CYS49 3.2 34.9 1.0
CB B:CYS59 3.3 35.7 1.0
CB B:CYS43 3.4 26.7 1.0
CB B:CYS62 3.4 28.4 1.0
O B:HOH202 3.8 36.2 1.0
N B:CYS49 4.1 37.6 1.0
CA B:CYS43 4.1 36.9 1.0
N B:CYS62 4.2 31.6 1.0
CA B:CYS49 4.2 39.4 1.0
O B:HOH204 4.4 45.5 1.0
CA B:ASN47 4.4 51.2 1.0
CA B:CYS62 4.4 30.0 1.0
N B:ASN47 4.5 45.8 1.0
N B:GLY45 4.7 34.9 1.0
CA B:CYS59 4.7 34.6 1.0
N B:ASP48 4.7 44.5 1.0
N B:ALA44 4.7 37.0 1.0
C B:CYS43 4.9 43.9 1.0
C B:ASN47 4.9 50.7 1.0

Zinc binding site 5 out of 8 in 4ond

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Zinc binding site 5 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:40.4
occ:1.00
 O E:HOH208 2.1 61.9 1.0
SG E:CYS59 2.3 38.5 1.0
SG E:CYS43 2.3 38.4 1.0
SG E:CYS62 2.4 39.3 1.0
SG E:CYS49 2.4 38.4 1.0
CB E:CYS49 3.2 42.6 1.0
CB E:CYS43 3.3 37.3 1.0
CB E:CYS59 3.3 32.9 1.0
CB E:CYS62 3.5 33.7 1.0
N E:CYS49 3.9 38.3 1.0
CA E:CYS43 4.0 34.4 1.0
O E:HOH203 4.2 35.2 1.0
CA E:CYS49 4.2 44.4 1.0
N E:CYS62 4.3 37.1 1.0
O E:HOH206 4.3 41.4 1.0
CA E:CYS62 4.5 41.6 1.0
CA E:ASN47 4.6 33.9 1.0
N E:ASP48 4.6 36.1 1.0
N E:ASN47 4.6 42.7 1.0
N E:ALA44 4.7 35.9 1.0
CA E:CYS59 4.8 34.8 1.0
C E:CYS43 4.8 38.5 1.0
O E:HOH216 4.8 53.3 1.0
C E:ASN47 4.9 36.5 1.0
N E:GLY45 4.9 38.3 1.0

Zinc binding site 6 out of 8 in 4ond

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Zinc binding site 6 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:44.3
occ:1.00
 SG E:CYS10 2.2 40.6 1.0
SG E:CYS24 2.3 44.0 1.0
SG E:CYS7 2.4 45.5 1.0
SG E:CYS27 2.5 45.3 1.0
CB E:CYS10 3.3 43.7 1.0
CB E:CYS7 3.3 46.0 1.0
CB E:CYS27 3.4 43.6 1.0
N E:CYS10 3.6 43.2 1.0
CB E:CYS24 3.6 37.7 1.0
N E:CYS24 4.0 42.6 1.0
CA E:CYS10 4.0 47.8 1.0
NH1 E:ARG56 4.2 53.1 1.0
N E:CYS27 4.2 42.0 1.0
CB E:ILE9 4.3 53.6 1.0
CA E:CYS24 4.4 40.0 1.0
CA E:CYS27 4.4 48.9 1.0
CB E:ASP12 4.6 59.0 1.0
C E:ILE9 4.6 51.9 1.0
C E:CYS10 4.7 52.7 1.0
N E:GLY11 4.7 52.0 1.0
CA E:CYS7 4.8 48.6 1.0
N E:ASP12 4.8 56.6 1.0
CA E:ILE9 4.9 50.1 1.0
N E:ILE9 5.0 50.1 1.0
CG2 E:ILE9 5.0 57.4 1.0

Zinc binding site 7 out of 8 in 4ond

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Zinc binding site 7 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:40.4
occ:1.00
 SG F:CYS59 2.3 36.3 1.0
SG F:CYS62 2.3 36.4 1.0
SG F:CYS49 2.4 38.0 1.0
SG F:CYS43 2.4 41.4 1.0
CB F:CYS49 3.2 39.1 1.0
CB F:CYS43 3.4 32.4 1.0
CB F:CYS59 3.4 38.7 1.0
CB F:CYS62 3.4 26.4 1.0
O F:HOH223 3.7 38.3 1.0
N F:CYS49 4.0 39.9 1.0
CA F:CYS43 4.1 37.7 1.0
N F:CYS62 4.2 31.4 1.0
O F:HOH204 4.2 40.5 1.0
CA F:CYS49 4.3 39.6 1.0
CA F:CYS62 4.4 36.6 1.0
CA F:ASN47 4.5 48.0 1.0
N F:ASP48 4.6 46.6 1.0
N F:ASN47 4.7 39.7 1.0
O F:HOH205 4.7 38.1 1.0
N F:ALA44 4.7 38.4 1.0
CA F:CYS59 4.8 42.8 1.0
C F:CYS43 4.8 40.7 1.0
N F:GLY45 4.8 39.4 1.0
C F:ASN47 4.9 49.7 1.0
O F:CYS59 5.0 33.6 1.0

Zinc binding site 8 out of 8 in 4ond

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Zinc binding site 8 out of 8 in the Ancestral Steroid Receptor 2 Dbd Helix Mutant - Ere Dna Complex


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 Dbd Helix Mutant - Ere Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn102

b:36.8
occ:1.00
 SG F:CYS10 2.2 40.0 1.0
SG F:CYS24 2.3 38.1 1.0
SG F:CYS7 2.4 36.3 1.0
SG F:CYS27 2.4 40.6 1.0
CB F:CYS7 3.3 28.7 1.0
CB F:CYS27 3.3 32.5 1.0
CB F:CYS10 3.4 35.6 1.0
CB F:CYS24 3.5 31.0 1.0
N F:CYS10 3.7 40.1 1.0
N F:CYS24 3.9 33.1 1.0
NH1 F:ARG56 4.0 45.5 1.0
CA F:CYS10 4.1 37.2 1.0
N F:CYS27 4.2 28.0 1.0
CB F:ILE9 4.3 43.2 1.0
CA F:CYS24 4.3 30.1 1.0
CA F:CYS27 4.4 33.2 1.0
CB F:ASP12 4.6 39.6 1.0
C F:ILE9 4.6 38.7 1.0
C F:CYS10 4.8 36.6 1.0
CA F:CYS7 4.8 29.9 1.0
N F:GLY11 4.8 34.2 1.0
CA F:ILE9 4.9 40.1 1.0
N F:ASP12 4.9 33.4 1.0
C F:CYS24 4.9 38.9 1.0
CG2 F:ILE9 4.9 33.9 1.0
N F:ILE9 5.0 46.1 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: Sun Oct 27 03:51:42 2024

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