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Zinc in PDB 4hc7: Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2

Protein crystallography data

The structure of Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2, PDB code: 4hc7 was solved by Y.Chen, D.L.Bates, R.Dey, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.765, 65.373, 72.922, 90.00, 96.75, 90.00
R / Rfree (%) 22.6 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2 (pdb code 4hc7). 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 Full Dna Binding Domain of GATA3-Complex 2, PDB code: 4hc7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4hc7

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Zinc binding site 1 out of 4 in the Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2


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 Full Dna Binding Domain of GATA3-Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:46.7
occ:1.00
SG A:CYS342 2.3 45.9 1.0
SG A:CYS339 2.3 28.7 1.0
SG A:CYS321 2.3 45.7 1.0
SG A:CYS318 2.6 51.6 1.0
CB A:CYS342 3.1 44.9 1.0
CB A:CYS318 3.2 49.1 1.0
CB A:CYS321 3.3 48.0 1.0
CB A:CYS339 3.4 34.0 1.0
N A:CYS321 3.5 50.3 1.0
N A:CYS339 3.9 38.6 1.0
CA A:CYS321 4.0 49.5 1.0
N A:CYS342 4.2 45.0 1.0
CA A:CYS339 4.2 37.0 1.0
CG2 A:THR323 4.2 42.7 1.0
CA A:CYS342 4.2 45.9 1.0
CB A:ASN320 4.4 51.4 1.0
NH1 A:ARG353 4.6 59.6 1.0
C A:CYS321 4.6 48.5 1.0
N A:GLN322 4.6 49.6 1.0
C A:ASN320 4.7 51.6 1.0
O A:CYS339 4.7 38.5 1.0
CA A:CYS318 4.7 47.5 1.0
C A:CYS339 4.8 38.8 1.0
CA A:ASN320 4.9 51.5 1.0
N A:ASN320 4.9 50.2 1.0

Zinc binding site 2 out of 4 in 4hc7

Go back to Zinc Binding Sites List in 4hc7
Zinc binding site 2 out of 4 in the Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2


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 Full Dna Binding Domain of GATA3-Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:55.2
occ:1.00
SG A:CYS288 2.3 42.8 1.0
SG A:CYS264 2.4 63.6 1.0
SG A:CYS267 2.4 55.5 1.0
SG A:CYS285 2.4 56.4 1.0
CB A:CYS288 3.1 41.6 1.0
CB A:CYS267 3.2 61.5 1.0
CB A:CYS264 3.2 73.5 1.0
CB A:CYS285 3.3 58.3 1.0
N A:CYS267 3.7 63.2 1.0
N A:CYS285 3.9 64.7 1.0
CA A:CYS267 4.0 62.0 1.0
NH1 A:ARG299 4.2 52.7 1.0
CA A:CYS285 4.2 59.6 1.0
N A:CYS288 4.2 43.5 1.0
CA A:CYS288 4.3 42.7 1.0
O A:HOH544 4.4 42.4 1.0
CB A:ALA269 4.5 68.3 1.0
CA A:CYS264 4.7 76.7 1.0
O A:CYS285 4.7 57.4 1.0
CB A:ASN266 4.7 64.8 1.0
N A:GLY268 4.7 63.3 1.0
C A:CYS267 4.8 62.6 1.0
C A:ASN266 4.8 64.7 1.0
C A:CYS285 4.8 56.7 1.0
N A:ALA269 4.9 68.1 1.0
ND2 A:ASN266 4.9 63.5 1.0

Zinc binding site 3 out of 4 in 4hc7

Go back to Zinc Binding Sites List in 4hc7
Zinc binding site 3 out of 4 in the Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2


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 Full Dna Binding Domain of GATA3-Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:70.2
occ:1.00
SG B:CYS339 2.3 57.2 1.0
SG B:CYS321 2.4 85.4 1.0
SG B:CYS318 2.4 78.7 1.0
SG B:CYS342 2.5 66.7 1.0
CB B:CYS318 3.0 79.4 1.0
CB B:CYS342 3.2 61.1 1.0
CB B:CYS339 3.3 57.3 1.0
CB B:CYS321 3.4 83.8 1.0
N B:CYS321 3.5 81.4 1.0
N B:CYS339 3.7 57.3 1.0
CA B:CYS321 4.0 83.4 1.0
CA B:CYS339 4.1 56.9 1.0
CG2 B:THR323 4.1 84.6 1.0
N B:CYS342 4.3 55.7 1.0
CA B:CYS342 4.4 59.1 1.0
CB B:ASN320 4.5 78.4 1.0
CA B:CYS318 4.5 79.3 1.0
N B:GLN322 4.6 85.3 1.0
C B:CYS321 4.6 84.8 1.0
O B:CYS339 4.6 56.7 1.0
C B:ASN320 4.7 79.9 1.0
C B:CYS339 4.7 56.4 1.0
NH1 B:ARG353 4.8 71.3 1.0
N B:ASN320 4.8 77.3 1.0
C B:VAL338 4.9 59.4 1.0
CA B:ASN320 4.9 78.8 1.0
N B:THR323 4.9 82.8 1.0

Zinc binding site 4 out of 4 in 4hc7

Go back to Zinc Binding Sites List in 4hc7
Zinc binding site 4 out of 4 in the Crystal Structure of the Full Dna Binding Domain of GATA3-Complex 2


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 Full Dna Binding Domain of GATA3-Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:53.8
occ:1.00
SG B:CYS285 2.3 38.5 1.0
SG B:CYS267 2.3 45.9 1.0
SG B:CYS288 2.3 39.1 1.0
SG B:CYS264 2.5 64.1 1.0
CB B:CYS288 3.2 43.0 1.0
CB B:CYS285 3.2 40.2 1.0
CB B:CYS267 3.3 48.5 1.0
CB B:CYS264 3.3 63.5 1.0
N B:CYS267 3.9 50.6 1.0
N B:CYS285 3.9 42.7 1.0
NH1 B:ARG299 4.1 58.1 1.0
CA B:CYS285 4.1 43.0 1.0
CA B:CYS267 4.1 50.3 1.0
N B:CYS288 4.2 44.8 1.0
CA B:CYS288 4.3 44.1 1.0
O B:HOH515 4.3 45.9 1.0
CB B:ALA269 4.4 55.1 1.0
O B:CYS285 4.6 45.4 1.0
C B:CYS285 4.7 44.2 1.0
CA B:CYS264 4.8 63.2 1.0
N B:GLY268 4.8 52.8 1.0
CB B:ASN266 4.8 51.4 1.0
N B:ALA269 4.9 52.0 1.0
C B:CYS267 4.9 51.6 1.0
C B:ASN266 4.9 51.2 1.0
ND2 B:ASN266 5.0 51.8 1.0

Reference:

Y.Chen, D.L.Bates, R.Dey, P.H.Chen, A.C.Machado, I.A.Laird-Offringa, R.Rohs, L.Chen. Dna Binding By Gata Transcription Factor Suggests Mechanisms of Dna Looping and Long-Range Gene Regulation. Cell Rep V. 2 1197 2012.
ISSN: ESSN 2211-1247
PubMed: 23142663
DOI: 10.1016/J.CELREP.2012.10.012
Page generated: Wed Dec 16 05:21:57 2020

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