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Zinc in PDB 1r0o: Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding Complex

Protein crystallography data

The structure of Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding Complex, PDB code: 1r0o was solved by S.Devarakonda, J.M.Harp, Y.Kim, A.Ozyhar, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.77 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.370, 59.880, 113.770, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding Complex (pdb code 1r0o). 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 the Heterodimeric Ecdysone Receptor Dna-Binding Complex, PDB code: 1r0o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1r0o

Go back to Zinc Binding Sites List in 1r0o
Zinc binding site 1 out of 4 in the Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding 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 the Heterodimeric Ecdysone Receptor Dna-Binding Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn351

b:40.9
occ:1.00
SG A:CYS27 2.2 34.5 1.0
SG A:CYS24 2.3 29.4 1.0
SG A:CYS10 2.4 31.4 1.0
SG A:CYS7 2.4 35.9 1.0
CB A:CYS27 3.1 34.3 1.0
CB A:CYS7 3.4 39.3 1.0
CB A:CYS24 3.5 31.1 1.0
CB A:CYS10 3.5 32.8 1.0
N A:CYS10 3.8 34.6 1.0
N A:CYS27 4.0 31.5 1.0
N A:CYS24 4.0 36.7 1.0
CA A:CYS27 4.1 33.8 1.0
CA A:CYS10 4.3 32.9 1.0
CA A:CYS24 4.3 34.1 1.0
NH1 A:ARG56 4.3 30.6 1.0
CB A:ILE9 4.3 33.8 1.0
CB A:ASP12 4.5 35.6 1.0
CG2 A:ILE9 4.5 35.4 1.0
NH2 A:ARG63 4.7 29.7 1.0
C A:ILE9 4.7 36.0 1.0
O A:CYS24 4.8 31.6 1.0
CA A:CYS7 4.9 41.6 1.0
C A:CYS24 4.9 32.8 1.0
CD A:ARG56 4.9 32.2 1.0
CA A:ILE9 5.0 35.8 1.0
N A:ASP12 5.0 34.2 1.0
C A:CYS10 5.0 32.3 1.0

Zinc binding site 2 out of 4 in 1r0o

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Zinc binding site 2 out of 4 in the Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding 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 the Heterodimeric Ecdysone Receptor Dna-Binding Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn353

b:50.2
occ:1.00
SG A:CYS62 2.3 41.3 1.0
SG A:CYS43 2.3 49.9 1.0
SG A:CYS59 2.4 41.0 1.0
SG A:CYS49 2.5 38.3 1.0
CB A:CYS43 3.2 50.2 1.0
CB A:CYS49 3.3 38.5 1.0
CB A:CYS59 3.3 37.8 1.0
CB A:CYS62 3.4 37.1 1.0
CA A:CYS43 4.0 52.0 1.0
N A:CYS62 4.2 38.2 1.0
N A:CYS49 4.2 45.4 1.0
O A:HOH357 4.2 40.4 1.0
O A:ASN46 4.3 60.7 1.0
CA A:CYS49 4.3 42.1 1.0
CA A:CYS62 4.4 37.6 1.0
O A:HOH433 4.4 39.7 1.0
CA A:ARG47 4.4 54.9 1.0
C A:ASN46 4.7 58.9 1.0
CA A:CYS59 4.7 37.8 1.0
N A:ASN48 4.8 53.1 1.0
N A:ARG47 4.8 57.1 1.0
O A:HOH381 4.9 35.5 1.0
C A:CYS43 4.9 54.0 1.0
C A:ARG47 4.9 53.9 1.0
CB A:TYR61 4.9 38.7 1.0
CD2 A:TYR61 4.9 38.7 1.0
N A:ARG44 4.9 56.6 1.0

Zinc binding site 3 out of 4 in 1r0o

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Zinc binding site 3 out of 4 in the Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding 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 the Heterodimeric Ecdysone Receptor Dna-Binding Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn350

b:38.6
occ:1.00
SG B:CYS27 2.3 26.3 1.0
SG B:CYS10 2.4 26.6 1.0
SG B:CYS24 2.4 26.1 1.0
SG B:CYS7 2.6 31.1 1.0
CB B:CYS27 3.3 25.5 1.0
CB B:CYS10 3.4 27.3 1.0
CB B:CYS7 3.5 30.6 1.0
CB B:CYS24 3.6 26.5 1.0
N B:CYS10 3.7 28.7 1.0
N B:CYS24 4.0 25.9 1.0
N B:CYS27 4.0 26.4 1.0
NH1 B:ARG56 4.1 22.4 1.0
CA B:CYS10 4.1 28.5 1.0
CA B:CYS27 4.2 27.0 1.0
CB B:VAL9 4.3 27.3 1.0
CA B:CYS24 4.3 25.7 1.0
CB B:ASP12 4.5 29.4 1.0
NH2 B:ARG63 4.8 23.3 1.0
C B:VAL9 4.8 28.9 1.0
CG1 B:VAL9 4.8 24.7 1.0
CD B:ARG56 4.8 24.1 1.0
C B:CYS10 4.8 27.8 1.0
C B:CYS24 4.9 27.5 1.0
CA B:CYS7 4.9 33.9 1.0
N B:ASP12 4.9 30.3 1.0
O B:CYS24 4.9 28.1 1.0
N B:GLY11 5.0 29.7 1.0
CA B:VAL9 5.0 27.3 1.0

Zinc binding site 4 out of 4 in 1r0o

Go back to Zinc Binding Sites List in 1r0o
Zinc binding site 4 out of 4 in the Crystal Structure of the Heterodimeric Ecdysone Receptor Dna-Binding 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 the Heterodimeric Ecdysone Receptor Dna-Binding Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn352

b:50.3
occ:1.00
SG B:CYS59 2.3 31.0 1.0
SG B:CYS62 2.3 34.7 1.0
SG B:CYS49 2.4 34.6 1.0
SG B:CYS43 2.5 43.6 1.0
CB B:CYS62 3.2 29.2 1.0
CB B:CYS43 3.2 42.4 1.0
CB B:CYS49 3.2 37.5 1.0
CB B:CYS59 3.4 30.2 1.0
N B:CYS49 3.9 43.6 1.0
N B:CYS62 4.1 31.2 1.0
CA B:CYS43 4.2 44.7 1.0
CA B:CYS49 4.2 39.3 1.0
CA B:CYS62 4.2 30.1 1.0
CA B:ARG47 4.4 55.5 1.0
N B:ARG47 4.4 55.8 1.0
O B:HOH375 4.4 41.2 1.0
CD1 B:PHE45 4.4 49.6 1.0
N B:ALA48 4.5 51.0 1.0
CB B:PHE45 4.6 50.8 1.0
C B:ARG47 4.7 53.8 1.0
CA B:CYS59 4.8 29.4 1.0
C B:CYS43 5.0 46.5 1.0

Reference:

S.Devarakonda, J.M.Harp, Y.Kim, A.Ozyhar, F.Rastinejad. Structure of the Heterodimeric Ecdysone Receptor Dna-Binding Complex Embo J. V. 22 5827 2003.
ISSN: ISSN 0261-4189
PubMed: 14592980
DOI: 10.1093/EMBOJ/CDG569
Page generated: Wed Dec 16 03:02:12 2020

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