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Zinc in PDB 1r4i: Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element

Protein crystallography data

The structure of Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element, PDB code: 1r4i was solved by P.L.Shaffer, A.Jivan, D.E.Dollins, F.Claessens, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.890, 137.890, 85.710, 90.00, 90.00, 120.00
R / Rfree (%) 24.6 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element (pdb code 1r4i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element, PDB code: 1r4i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1r4i

Go back to Zinc Binding Sites List in 1r4i
Zinc binding site 1 out of 4 in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element


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 Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn650

b:86.3
occ:1.00
SG A:CYS562 2.2 87.8 1.0
SG A:CYS545 2.2 99.4 1.0
SG A:CYS542 2.4 0.5 1.0
SG A:CYS559 2.4 93.4 1.0
CB A:CYS545 2.8 97.8 1.0
CB A:CYS559 2.9 95.5 1.0
N A:CYS545 3.0 96.8 1.0
CB A:CYS562 3.2 90.5 1.0
CA A:CYS545 3.5 98.7 1.0
CB A:CYS542 3.5 0.9 1.0
N A:CYS559 3.5 95.6 1.0
CA A:CYS559 3.8 96.6 1.0
CG2 A:ILE544 3.9 92.9 1.0
CB A:ILE544 4.0 94.4 1.0
C A:ILE544 4.1 95.9 1.0
N A:GLY546 4.3 0.6 1.0
C A:CYS545 4.4 0.3 1.0
CA A:CYS562 4.4 91.3 1.0
N A:CYS562 4.5 92.5 1.0
CA A:ILE544 4.5 95.2 1.0
NH1 A:ARG591 4.6 0.3 1.0
C A:CYS559 4.7 97.2 1.0
C A:THR558 4.7 94.6 1.0
N A:ILE544 4.8 95.6 1.0
O A:CYS559 4.9 97.7 1.0
NH2 A:ARG598 4.9 82.4 1.0
CA A:CYS542 4.9 0.6 1.0
CA A:THR558 5.0 93.5 1.0

Zinc binding site 2 out of 4 in 1r4i

Go back to Zinc Binding Sites List in 1r4i
Zinc binding site 2 out of 4 in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element


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 Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn651

b:89.2
occ:1.00
SG A:CYS584 2.2 0.6 1.0
SG A:CYS578 2.2 0.6 1.0
SG A:CYS594 2.3 98.5 1.0
SG A:CYS597 2.5 95.5 1.0
CB A:CYS594 2.9 94.8 1.0
CB A:CYS578 3.5 0.9 1.0
CB A:CYS584 3.6 0.8 1.0
CB A:CYS597 3.7 95.8 1.0
N A:ALA579 3.8 0.5 1.0
CA A:CYS578 3.8 0.1 1.0
C A:CYS578 4.3 0.0 1.0
CA A:CYS594 4.3 94.0 1.0
N A:CYS597 4.4 95.8 1.0
N A:CYS584 4.5 0.4 1.0
CA A:CYS597 4.7 95.2 1.0
CA A:CYS584 4.7 0.1 1.0
N A:SER580 4.8 0.4 1.0
N A:ASN582 4.8 0.9 1.0
CA A:ASN582 4.9 0.7 1.0
CA A:ALA579 4.9 0.3 1.0
N A:ASP583 5.0 0.0 1.0
C A:CYS594 5.0 92.7 1.0

Zinc binding site 3 out of 4 in 1r4i

Go back to Zinc Binding Sites List in 1r4i
Zinc binding site 3 out of 4 in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element


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 Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn652

b:95.8
occ:1.00
SG B:CYS562 2.1 0.5 1.0
SG B:CYS545 2.4 0.3 1.0
SG B:CYS542 2.5 0.8 1.0
SG B:CYS559 2.5 0.2 1.0
CB B:CYS545 3.0 0.9 1.0
CB B:CYS562 3.0 0.8 1.0
CB B:CYS559 3.0 0.5 1.0
N B:CYS545 3.2 0.4 1.0
N B:CYS559 3.3 0.1 1.0
CB B:CYS542 3.5 0.9 1.0
CA B:CYS545 3.6 0.4 1.0
CA B:CYS559 3.8 0.9 1.0
CG2 B:ILE544 3.8 0.7 1.0
CB B:ILE544 3.8 0.2 1.0
CA B:CYS562 4.2 0.9 1.0
C B:ILE544 4.2 0.2 1.0
NH1 B:ARG591 4.3 0.6 1.0
N B:CYS562 4.4 0.7 1.0
N B:GLY546 4.4 0.8 1.0
C B:THR558 4.4 0.2 1.0
CA B:ILE544 4.5 0.4 1.0
C B:CYS545 4.5 0.8 1.0
N B:ILE544 4.6 0.4 1.0
CA B:THR558 4.6 0.2 1.0
C B:CYS559 4.7 0.4 1.0
O B:CYS559 4.9 0.1 1.0
CA B:CYS542 4.9 0.8 1.0
NH2 B:ARG598 5.0 98.8 1.0

Zinc binding site 4 out of 4 in 1r4i

Go back to Zinc Binding Sites List in 1r4i
Zinc binding site 4 out of 4 in the Crystal Structure of Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element


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 Androgen Receptor Dna-Binding Domain Bound to A Direct Repeat Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn653

b:88.3
occ:1.00
SG B:CYS584 2.3 0.3 1.0
SG B:CYS597 2.3 0.2 1.0
SG B:CYS594 2.4 0.7 1.0
SG B:CYS578 2.5 1.0 1.0
CB B:CYS594 3.0 0.7 1.0
CB B:CYS584 3.1 0.1 1.0
CB B:CYS597 3.3 0.5 1.0
CB B:CYS578 3.7 0.3 1.0
CA B:CYS578 4.1 0.0 1.0
N B:CYS597 4.2 0.2 1.0
CA B:CYS597 4.3 1.0 1.0
N B:ALA579 4.4 0.3 1.0
CA B:CYS584 4.4 0.2 1.0
CA B:CYS594 4.5 99.9 1.0
N B:CYS584 4.6 0.1 1.0
O B:CYS594 4.7 97.7 1.0
CA B:ASN582 4.7 0.1 1.0
C B:CYS578 4.8 0.6 1.0
N B:ASN582 5.0 0.1 1.0
C B:CYS594 5.0 99.0 1.0

Reference:

P.L.Shaffer, A.Jivan, D.E.Dollins, F.Claessens, D.T.Gewirth. Structural Basis of Androgen Receptor Binding to Selective Androgen Response Elements. Proc.Natl.Acad.Sci.Usa V. 101 4758 2004.
ISSN: ISSN 0027-8424
PubMed: 15037741
DOI: 10.1073/PNAS.0401123101
Page generated: Wed Dec 16 03:02:27 2020

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